To your first question: an IntuiFace project doesn't know if Composer is 32-bit or 64-bit so yes, it's interchangeable. There are some features from Version 5.x that were 32-bit and were dropped from Version 6 - like out-of-the-box RFID support, or the legacy Web Browser option or 32-bit dlls. But if you build it in Version 6, you can go back and forth between 32-bit and 64-bit.
I can't speak about the complexity of giving people the option in the installer but I do know we erred on the side of caution and not let people try to install 64-bit apps on a 32-bit PC. We'll continue to evolve the installer so it'll get smarter and thus. long term, it should also be more flexible.