Does anyone know the method plex uses to detect the ROMs? Is it just matching names or does it for further than that?
magic and special sauce 
combination of names, extensions, CRCs, etc.
I figured as much! Lol. I was having trouble with my Sega roms. They were all .bin files, renamed one to .gen and it showed up. Hope they will expand on the article about naming them to help with troubleshooting such things.
they use the md format for megadrive/genesis roms