From the sound of things you can very well be a real winner.
My concern about unit replacement was based upon a shop who diagnoses by unit exchange. I pointed out that reverse clutch job should also include all seals and other clutches - often known as a rebuild! if your shop does enough of these that they have one in a more efficient point for installation in your car I have absolutely no problem with that.
Anyone doing these things regularly will only have one problem with them. That is small shift irregularities. These can require valve bodies and even a case can get warpage or internal leaks. This is very rare and everything else is staright nuts and bolts to get it mechanically right. If he fails he will notice it and maybe in some cases not notice till driven a while. This second set of conditions is the real risk in tranny repair and if the thing accepts adjustment it will last forever (which is 100,000 miles according to lifetime tranny oil requirements).
A shop doing that amount of tranny work should give the best value. As long as the basic tranny numbers are right don't worry about which tranny you got. If its working good you're a winner!
Bosch Master, ASE Master, L1
33 years MB technician