Lurch, JimDrew is actually working on the FPGA arcade, Im just following the project (and got to see the actual board a year ago).
Anyhoo, the FPGA is NOT (yet) the ultimate Amiga setup that gives a 060 equipped 1200 a kicking.
It is an attempt to to a very exact reimplementation of the original A1200, improving speed only where it doesnt break compatibility.
Remember, the Amiga will barely boot from a 060 without stuff like cyberpatcher.
So any software that uses the FPU or any specific 040 or 060 instructions is not likely to work with the FPGA arcade, much like a "vanilla" a1200 wouldnt.