i wouldnt give up on FBA codebase, afterall, were using an alpha version of the emu so i think i can safely assume things arent finalized. i still remember when i was trying to add support kof2knd for FBA 02.94.97 (the 512kb S rom doesnt extract) then 02.94.98 was released with everything now possible (including decrypted C sets even without S ROMs).
MAME also seems to have taken change in their Neogeo and CPS/2 driver structure as the time passed (from .64 if im not mistaken to recent).