So from what I’ve read elsewhere it may be possible to get what I want. First I need to switch from what I think is the default FBA emulator – PiFBA – to the retroarch compatible one – PiFBA libretro.
Since these use different romsets some work will be required to fix the roms but that’s generally simple, if not quick.
Once that’s done I need to use per game overrides to force certain games to use alternative button mapping. (http://blog.andressm.org/new-retroarch-features-2/)
How do I switch from PiFBA to FBA-libretro?