Sounds like you’ve figured out most of the problems. The HDMI thing might be an overscan issue in raspi-config but if not, then kitchuk’s guidance is probably best.
none of the ROMS on the pi can be compressed. It won’t see them. This is because performance would be incredibly hampered by on the fly decompression.
I do think we should have a different system for saves and game libraries, but this isn’t something I can advocate for much since I can’t program in c/c++ :P