I think retropie is in a position to help steer rom management to a more modern approach
simply having a directory with rom related files would be easy to manage
/home/pi/roms/nes (or wherever, even /opt/emu/nes/)
./../snake-rattle-and-roll.nes/program.rom (or .nes for first approach)
./../snake-rattle-and-roll.nes/manifest.xml
./../snake-rattle-and-roll.nes/artwork.png
./../snake-rattle-and-roll.nes/game-save.sav
./../snake-rattle-and-roll.nes/retropie.cfg
./../snake-rattle-and-roll.nes/artwork-square.png
./../snake-rattle-and-roll.nes/cheats.cheat
./../snake-rattle-and-roll.nes/controller.cfg (likely unnecessary)
we could still put screenshots and extra fun stuff in /home/pi/;
this would help for easier management of game related files, without multiple locations for things; it would properly treat the games with the respect they deserve; and promote a true attempt at durable preservation of retro games we love so much.