Is there any functional difference between the older phosphate black 22lr bolts and the new stainless version?
Were there different generations of the design, or was it just a change in the finish?

There were some slight differences (firing pin retainer was changed to a cotter pin at some point, extractor channel was slightly smaller on the old ones, etc.).  Whether or not that makes any difference in function depends on what you are trying to do (and what new parts you are using with it).

there is a difference in the lengths of the collar units, that could cause problems...I replaced my A model phosphate chamber unit with a B collar unit and dedicated 16" barrel around 2010, and a second unit followed with a 9" dedicated barrel when I got my SBR stamp... the older collars are .675" long and the newer collars .700"... an short collar used on a longer newer stub barrel will shoulder on the feed ramp, and not the front of the collar... repeated firing can shear the feed ramp off... CMMG quickly replaced mine with a new collar.. regards

Thanks, I’ve been wanting a dedicated upper and had a chance to pick up one of the older CMMG M4 uppers with the dark bolt.
If it will mean trouble down the road if I want to swap out parts or upgrade the bolt for reliability I might just wait and build up from scratch around my stainless conversion bolt.