I suppose you are saying that the cylinder is recessed so that the case heads are enclosed on the sides as in the old S&W revos. That has zero effect on headspace or case support. It is a cosmetically desirable feature for some folks who swoon over such examples of gun building. S&W eliminated that as a cost saving measure. Guns cut for moon clips have more cut away for clip clearance.
Is the new cylinder the same outside diameter as the existing cylinder? If it is substantially smaller, that would be a bad sign.
Key to all of this is to, first, determine if the cylinder is adequate in diameter/cylinder wall thickness and can be properly fit to the frame. You might have to fit a new base pin bushing to help set endshake and headspace. If you can't buy one, a machinist can turn one easily enough. Once the cylinder is properly fit, then and only then can you proceed with reaming the chambers and throats to 45 dimensions. The proper reamer will be revolver specific. Do not use one made for an automatic. They are different.
The 45 headspaces off the case mouth. The rim is .049"-.010" (.039"-.049") thick. Rim diameter is .480"-.010" (.470"-.480"). Case diameter is .476" at the base.
The .44 Magnum headspaces off the rim. The rim is .060"-.011" (.049"-.060") thick. Rim diameter is .514"-.010 (.504"-.514"). Case diameter is .457" at the base. Headspace dimension is .060"-.070" on 44 Mag revos.
So, based on the fit of your new cylinder to the frame, ream the chambers to minimum headspace for 45 ACP and you are left with .011" (best case) to .031" (worst case) of case exposure ahead of the rim. If you were to ream to max headspace (why?), then add .020" to those measurements. You would likely start having ignition problems at that point. As for the case exposure, a standard GI issue 45 has more than that under normal circumstances. The safe unsupported case exposure on the 45ACP is .250"-.260". That is in a gun that can have wildly different static and dynamic headspace.
You might be able to use moon clips with this depending on just how close in dimension your cylinder is to the S&W N frame 45ACP.
These are just general thoughts in no specific order. The order of work will be determined by what you have and where you're going, but must start with pre-fitting of the cylinder and measurements.
Lots of measuring. Lots....