The having too many files problem that you encountered is specific to Magician Lord. I need to change how the site works to accomodate the two input roms. I didn't consider both zips would have the same rom it needs, so it grabbed both, then said wait a minute there's too many. That is an easy fix though.
It uses the sha of the rom file (not the zip, the roms inside of it), to look for the roms it needs. So usually it doesn't care about extra files, it just ignores them. Just about any mame neo geo rom will work because, at least in my experience, the mame dumps for neo geo games have not changed in a very long time.
Yeah there's tons of different neo roms floating around, and the contents of the zip varies a lot. But the actual rom files themselves are the same in all the zips. Again, at least in my experience with the other games (kof94, ss4, lb and puzzle bobble).