I know that some of haberman's libraries (like upb) include JIT compilers. In those cases you can't just rely on the compiler to take care of instruction set differences. (I'm on the mobile Firefox team, and we run into similar issues targeting our JavaScript engine to different ARM flavors.)
Then that very well could turn out to be a complete nightmare!
Yes, if you're in the business of writing compilers - traditional, JIT or otherwise - then you're going to hit all sorts of issues with this stuff, and rapidly head off beyond the realms in which I have anything useful to say :)
