Hi! I'm an admin from RetroAchievements, excited to see all the hype around here. Each achievement set will have specific files it supports, as visible in "supported game files". In the case of Earthbound, that encompasses a wide variety of translations as well as a few improvement hacks, plus the basic US version of the game. Usually games will have a much smaller number of supported files due to incompatibilities in the memory across versions complicating matters, as well as the achievement set dev being responsible for ensuring compatibility with the linked files. That said, hashing is based on the rom file itself, not the filename. In the case of SNES in particular, it's just an md5 hash of the (headerless) game file. Different romhacks may have their own sets, and there are some special inert patches available to enable challenge achievement sets, such as one for completing the game while avoiding the cameraman at every opportunity.

If you have any further questions, please don't hesitate to ask!