Sounds like your issue lies in having too many clones which can be managed more effectively with a building a merged set with clrmamepro:
https://github.com/RetroPie/RetroPie-Setup/wiki/Managing-ROMs#step-5–rebuild-a-rom-set
I would think that the filenames are out of the bounds of theme management and are rather a core emulationstation function which is much more of a headache to sort than a few xml files.