Instead of there being 8 main categories (Any% and 100% for all 4 versions) it could just be setup to where there are just 2 categories (Any%/100%) with sub categories for versions under them.

This can be done with the "extra variables" in the settings. Just make a variable called Version and have it apply to full-game and all categories, then make the list of versions and set one to be the default. Then check the option "use as sub category".

Also as far as I'm aware only the Genesis version is different (because of sprint allowing you to move twice as fast). NES/PC/Gameboy all should be the same unless there's something I don't know about?

I've also done a 100% run on Genesis in 1:00:20