One thing I could do is make it so that when you submit a run for this game, you'll specify whether you played it on the "web" or "pc" platform, with "pc" meaning the Steam version. I can then tell the leaderboard to make the different platforms not obsolete each other. Does that sound like a good solution?
looking over the differences from the link, i'll just say, screw it why not, new categories. it would probably make 100% completely different, while any% dont think that would change to much.
some differences are substantial enough to warrant a different category, therefore it will happen.
one thing to note is that the steam version has a NG+ so that might also become a different category.
me from 2 years ago doesn't know how to handle a forum, yeesh. I'm locking this thread. 2 years late but oh well.