Unfortunately it makes dealing with MAME a huge fucking pain in the ass.

The MAME community does this because they think of themselves as an 'archiving' community rather than just an 'emulation' community so they want their ROMs to as accurate a rendition of the original arcade boards as possible. It's usually just because some of the individual chip images within the zipped ROM have been renamed or something small like that, but it totally breaks compatibility. It's because every time MAME gets updated, some of the ROMs that worked with the older version will no longer work.