Howdy Mako, I'll try to answer the question you seem to be asking about the arbor bottoming but specifically the cylinder gap area. I think this part is misunderstood by many. The looseness in the arbor hole with the arbor in it seems to almost always be along the top of the arbor. When the barrel is drawn back by the wedge the bottom lug of the barrel stops at the frame but the top breech end of the barrel doesn't stop even with it. The breech of the barrel keeps going back closing the cylinder gap abiet unevenly. The gap gets closer at the top of it and wider at the bottom of it as you observe from the side seeing light come thrrough. That's because the force of the wedge has to go somewhere and the path of least resistance is anywhere there's space. The space is at the top of the arbor and is seen at the top of the barrels arbor hole. The barrel can't go anywhere at the bottom lug since there's no space there if the barrel is against the frame. So as the space is closed at the breech area with the barrel canting downward at the breech end and naturally upward at the muzzle end until the top of the barrels arbor hole right at the beginning cants downward until contact is made by the top of the barrels arbor hole at the very beginning with the top of the arbor. That contact point and the space there being closed up then the barrel stops moving. You know...like the barrel pivots at the frame/barrel point stressing the frame pins when those holes in the barrel take up any space that's there and the pins can flex some until the space at the top of the arbor hole at the beginning of the barrels arbor hole is closed and the barrel is in contact with the top of the arbor there. That rocking or canting of the barrel after the barrels bottom lug contacts the frame is the movement that eludes a lot of people.
The guns that have more space in the arbor hole than others also shoot higher than the others with less space. Also the guns with the most space in the arbor hole of the barrel when the arbor is in there have a cylinder gap wider at the bottom and naorrower at the top of it. Take Ubertis for example....the ones people say they have to set the cylinder gap with a feeler gauge at each assembly. Those have more space at the top of the arbor hole and they can more easily have the wedge force close the gap and pinch the cylinder and stop it from moving. The Piettas then....have a more snug arbor hole for the arbor to fit in and the minimal space is taken up and the top of the barrels arbor hole at the very beginning males contact with the top of the arbor and the barrel stops moving much sooner. It isn't only the bottomed arbor the Piettas have that sets the barrels rock solid and the wedges stop with a certain authority that can't be mistaken.When the wedge is driven into a Pietta Colt(the ones that are right from the factory) it goes so far and stops rock solid and it's real easy to tell it aon't going any further...doesn't cant enough to notice and doesn't pinch the cylinder and the cylinder gap is uniforn at the top of it and the bottom of it(at least uniforn enough it would be difficult to measure with a feeler gauge).
Anyway if a person doesn't realize the barrel is drawn back by the wedge with that tightening the barrel/frame contact but the breech part still moves until the top of the arbor hole space closes until the barrel at the top of that hole contacts the top of the arbor then it's difficult to fully understand the fit of a Colt type gun with a wedge and all. If a person doesn't realize there's movement by the barrel after the barrels bottom lug meets the frame they don't have the full picture. It's easy to miss I guess.
Take a Uberti since they are good examples......set the barrel on and push it rearward as far as you can....put pressure on the barrel as if you were trying to bend the barrel muzzle upwards and watch the space between the breech and the cylinder and the space between the top of the arbor hole in the barrel and the top of the arbor. When the wedge is out and you can move it by hand you can see it plain as day. If you can't believe the barrel cants upward at the muzzle and downward at the breech after the barrels bottom lug meets the frame then you won't ever see what's being discussed here.
You mentioned shim...and interprete myself talking about "side shims". No side shims. That would be kid of difficult with the wedge in there and all. I mention that a shim layed on the "top" of the arbor" and inserted with the arbor into the barrels arbor hole takes up the space there and seats the barrel much better and locks it better and the gun shoots less high ect.ect. Belgian Centenniasls and Piettas are examples. The Piettas or Centaure Centennials don't shoot as high out of the box as a Uberti(at least the older Ubertis since I can't talk about the newer ones I haven't seensince Beretta runs the show) because they have the arbor bottoms in the barrels hole and, in some cases also have a snug fit of the arbor in the barrels arbor hole. Optimum is a snug tap on or push on fit of the barrel on the arbor.
Mechanically speaking..if a barrel has a nice snug fit onto the arbor with "no space" in the hole,or very minimal, that is actually a better fitting than a bottomed arbor in the barrels hole. If a barrel is quite snug on the arbor with it's contact points being at the frame/barrel point and along the length of the arbor there's no where for the barrel to go once it stops at the frame/barrel point. It stops rock solid with no canting of the muzzle upwards and the breech downward. Mechanically speaking the arbor real nice and snug in the barrels arbor hole is better than just a bottomed arbor with space between the top of the arbor and the barrel. Why? Even with a bottomed arbor where the end of the arbor is perpendicular with the axis of the arbor and the bottom of the barrels hole is perpendicular with the axis of the barrel the barrel will still find a way to rock on the frame where the pins are until the space between the top of the arbor and the beginning of the hole is closed. It will at least stress the frame pins or let the pins move in the barrels holes or deform the pins ect.ect. untill the space between the arbor and the beginning of the barrels arbor hole is closed.
Anbywhooo......once it's all seen it becomes vdry simple. Like....crap...why didn't I see that before?

Even pro gunsmiths that are familiar with all types of complicated shooting machines can miss parts of the fitting of a barrel onto an Open Top Colt.
Anyway....if you put your barrel on your Colt and leave the wedge out and play with it and kind of move things around you'll see what I mean.
You will see that the perfect fit would be a very snug fit of the arbor in the barrels hole and a bottomed arbor in the hole See that the less space there is in the arbor holw when the arbor's in it the better and the bottomed arbor is only part of the fix. The space above the arbor being closed is as important as a bottomed arbor or maybe more so. The bottomed arbor is great but...without the minimum space between the arbor and the barrels hole the bottomed arbor is incomplete.
Anywhoooo.....so can see that the barrel still moves after the barrel meets the frame when the's a loose arbor hole.
Cylinder gap? I like to set those at .006-7 but sometimes .010 even. It's an opinion thing I guess as to what the optimum cylinder gap is. It matters what you do with the gun..Cowboy Shooting versas target shooting as an example. It depends on the gun too. I like the .006 but I gunsmith the guns for optimum accuracy which is just where my head is I guess. If I do a gun for someone and they are going to shoot "Cowboy Shooting" I'd be more apt to ask if they want a wider cylinder gap. A wider gap makes the standard diviations go up more.
Anyway....the shim of a softer than steel material(metal) is an easy fix. No need to bottom the arbor and all. Just get a shim in tight where you tap the barrel on with a rubber hammer(at least till the shim loosens up some which they do and need changed every so often after so many hundreds of balls fired. Maybe every 1,000 or 2,000 balls.) to form fit it. You know an aluminum or copper shim. If the shim is steel it will last a very long time but it has to be exactly the right thickness right off the bat.
It's actually better the go beyond the shim thing where the shim is cut with a pair of scissors and all and......
Put a dab of weld in two spots on the arbor. One where it wuld be just inside the beginning of the barrels arbor hole and the other neat the end of the arbor. File fit them to where the barrel goes on but goes on pretty snug. That is better than a shim that may get "lost" as you mentioned.
The dabs of weld on the arbor?........they can be used to get a gun shooting center instead of left or right or high or low to a certain degree ect.ect. also.
Anywhoo....epoxy type stuff to fill the space where the arbor doesn't bottom?

There's such a tremendous force emmitted by a wedge that it would crush the JB Weld or compress the epoxy. Wedges emitt a very large amount of force. The end of the arbor needs to be steel or it will just not do what a bottomed arbor does....stop the barrel rock solid.......if the bottom of the arbor hole is perpendicular with the barrels axis and the end of the arbor is perpendicular with the axis of the arbor then the bottomed arbor helps the barrel be mounted straight and more solid and have less movement when the gun fires.
Movementwhen the gun fires? Yep but I ain't got the energy to type about that.

Lets just say that the frame pins fit in the barrel holes and the wedges "fit" side to side and"top and bottom" are important to eliminate parts movement when the gun fires and important to optimum accuracy.
If a Colt gun is constructed or machined or fit together real well and proper it can shoot as accurately as any Remington cap&baller. Could be used as a target gun against Remingtons and Rodgers and Spencers ect.ect.
What you say? That guy is freekin nuts?
One thing.....
Just remember I told ya......the optimum fit of a Colts barrel has no space in the arbor hole and the arbor is bottomed in the hole.
Before I go........someone mentioned that they bevel the end of the arbor to fit better because the bottom of the hole is concave. Not good to do. The part of the end of the arbor that does the best bottoming job is the outside edge of the arbors end. The outside edge of the end of the arbor contacts the outside edge of the bottom of the hole. It's better to leave the end of the arbor as wide as it can be to contact the bottom of the hole as wide as it can. The bottom of the hole....around the outside of the circle or the "corner" is where the contact should be. Maybe the very small edge of the arbor gets beveled when it's a tight fit in the hole if the "corner" around the bottom of the hole has a slight radius to it and not a perfect 90 degree corner. Anyway the contact point is or has to be right arounf the edge of the arbor and the edge or corner of the hole where the hole very begins. The contct can go inward further from the edge or corner naturally. Some guns have the edge of the hole reamed at a 90 degree angle with the wall of the hole and that makes a step around the circumference of the hole for the arbor with an end perpendicular to the arbor to sit on. The center part of the hole can still be concave though.
Some guns have the bottom of the arbor hole reamed where the bottom is all flat and perpendicular to the walls of the hole. Anyway...don't bevel the end of the arbor unless it's to let it fit better where the bottom of the holes corner has a slight radius to it.
The in-between shim thickness? If it is a problem then the end of the arbor can be filed a little. The shims if there's only one that you want in the hole and it's a little thick can be stoned down some.
There's nothing wrong with a shim in the hole. I wouldn't want to mess with several shims in the hole though. Anyway..the shim can be fit to the circumference of the hole so that it stays in and doesn't fall out or get lost. It can be made to fall out too if that's what a person wants.
I think if a person uses the method of pressing the wedge in my hand or by a wood dowel and leaving it like that then the wedge is too loose. The barrel would go forward with the first shots and tighten against the wedge but the gap would get a little bigger and the wedge may loosen upon firing multiple shots. The wedge tapped with a small hammer handle or block of hardwood can seast the wedge with the correct tightness so the wedge stays there right where it's set to.
We all have our different and personal methods of doing things. Some are "right" enough and some are "right on". If a person is satisfied with their proceedures then that's all that matters as long as the gun shoots good enough for them.
Welds spots on the arbor and "wedging" the arbor between them? That's the idea. That's what the walls of the arbor hole does if the arbor fits right and is snug. Like in D. Chicoine's book,"Gunsmithing Guns of the Old West", he mentions that a snug push fit of the arbor into the arbor hole is a good thing.
Rotating the barrel on the arbor like is shown to see what type of bottoming space there is is a good thing. I post that from time to time for people. There's a little draw back though to that and that can't be used for a precise way to measure the amoung of bottoming needed. It's the looseness of the barrel on the arbor that causes a problem. You can move the barrel on the arbor and get two different measurements. The looseness of the arbor in the holes hole again........
You need a method that's more precise like using Prussian Blue(from Brownells) on the end of the arbor to tell when it's bottoming with too much space between the frame and barrel. Then stone the shim till the barrel comes to within a .001 or .002 of the frame. The .001-2 leaves room for "seat in" that accures when the arbor slot end or the barrels bottom of the hole compress from the wedge insetrtion and the force the wedge emmits. Shooting the gun can deform the end of the arbor a little after awhile too so the .001-2 is like a backup. Anyway the best way I've founf to bottom an arbor whether it be the actual end of a new arbor of a shim in the space is to get it close using Prussian Blue machinists ink (used like intetting blackening when working on wood) and seeing the gap between the barel and frame and then stoning the shim. Notice I'm saying shim and not shims. I like to end up with one shim in the hole so it can be tacked welded to the end if I want. It's cool to add material with welding and work that so when done the shim is actually the end of the arbor. Also...using the machists ink you can see if the whole arbor end ,or the full circumference of the edge of the arbor,is in contact with the bottom of the hole and if not stone the end so it is in better contact(before the barrel reaches the .001-002 space between the barrel and frame). A softer steel shim used in the hole can be left a tad wide and the barrel wacked with a rubber hammer to sest the shim. If not that then when the wedge sests the barrel and the wedge emitts it's great force the shim will flow in where there's any space and the entire end of the arbor will be in contact.
Anyway...if you're going to build a "race" Colt then the first thing is to have a machinist make an arbor that fits with no space in the "reamed uniform" barrels arbor hole. Then go from there. Make a wedge that is in contact with the barrels slot and the arbors slot that should be perfectly even with each other side to side and "top and bottom". That "top and bottom" keeps the barrel from rotating on the arbor. The barrel will do that even if the wedge is really really tight. The whole barrel and wedge can rotate up and down on the arbor. Put the barrel in a vise and grab the grip and rotate side to side. The barrel usually moves on the arbor as does the wedge in the slots. That space has to be taken up so the barrel can't move on firing and bounce side to side and wear the wedge and stress the arbor and change the point of impact of the balls on the target. People have a hard time imagining the barrel held on with a tight wede moving but it does every time the gun fires if there's any space to the fit of the pars at all. Then the flexibility of the arbor and the steel parts(stele has memory)is the only movement which can't be helped unless the parts are re-made of very hard ordanance grade steel to minimize the movement.
Now I'm done I guess. Hope this helps someone so all this typing is not for nothing. Mako...if I didn't answer your questions then let me know which ones I didn't answer.