I am now convinced that I know much less about emulation than I know about the German A2000 mobos!
But what software (other than certain versions of Setclock) would fail to run on A2000 vs. B2000 mobos? AFAIK the main reason to upgrade is for design bug fixes and hardware improvements rather than software compatibility.
P.S. Remember any software which requires 1MB of Chip memory is due to the ECS chip set upgrade rather than the B2000 spec.