I looked a bit into it and there don't seem to be any major differences, so I'd say the anniversary edition is okay, at least until someone points out a major difference. If there is some sort of difference that would result in a time loss or time save, then the anniversary runs will be moved to a different category, but until then I don't see anything wrong with using either version.

To be honest, I didn't expect anyone to still play this game, so I'm pleasantly surprised you took the effort to submit a speedrun. Sorry for the verification wait!