I'm not sure what point you're trying to make here. There will always be some code that doesn't work whenever you upgrade anything, usually because the programmer thought they were being clever but were in reality being stupid. Some A500 software stopped working if you put a memory expansion in. I guess then we shouldn't bother with memory expansions.
If any amiga software at all could be made to work on coldfire, I'd be happy, to be honest. If you just want to run old games that's fine, but I'm pushing the envelope here. Or pushing something, at any rate. My luck, probably. No need to whizz on my buzz.
Fortunately self-modifying code is rare, because on the whole it's difficult, dangerous and pointless. The biggest problem, as far as I gather, is opcodes that are still valid on Coldfire, but behave differently. That might be a problem, because they wouldn't throw an exception so you couldn't trap them. How often that would happen, I don't know. But UAE could be made to emulate coldfire I guess and we could try it there... worth giving it a shot, just to see what happens?