The entire top end [piston, cylinder, head, ...] can be swapped but the question would be why. If I have it right most people go the other way, put the CR parts on an MT for a performance increase.
That being said I may put an MT engine in my 74CR. I want to ride it an haven't been able to find an engine. I am a low performance rider so I don't need a high performance engine.
I also have both a 76 CR250 and MR250 with a couple of MR250 spare engines. The 76 CR came with a really busted up engine, bolt dropped down the intake and smashed up cylinder and crank case. Working on my aluminum welding skills right now. Haven't split the cases on the MRs yet but the top ends appear to be identical. Cranks are diff, small shaft for the CR magneto while the MR has a huge set up for running lights.