This most certainly is an issue. ROM Hacks are one thing, there are hundreds of variants and tbh LaunchBox with enough configuration can host all your hacked roms with custom fields quite beautifully in its current form. There is no reason to add 700 variants per NES title to the DB, thats insane.
But what I am suggesting is a feature to allow 'Bootleg Support'
Table the idea of all the different SMB and Super Metroid ROM hacks, but in the Arcade and Fighting Game community there are certain established variants that are part of the culture. Two prime examples would be: The King of Fighters '97 Plus & Crouching Tiger, Hidden Dragon 2003 Super Plus alternate, both for the Neo Geo AES. There is also dozens of Arcade fighters such as Street Fighter Alpha 2 and Alpha 3 that have a Phoenix Edition version which is both the acclaimed community version (based on what MAME dump you are playing) and the region free version most likely matching the real world board you play on.
These all lack representation in the Metadata DB. And I would think coming up with a solution to incorporate some Bootleg Support would clear up a few dozen "What do I do about 2 files with the same name" threads.