I am a little sceptical about this 5v FPGA compatibility issue. I think it is a non-issue. I've seen it quoted in in many MiniMig posts, but if the chip the FPGA is connecting to is TTL 5v (which I think Amiga chips are?) then 3.3v FPGA's will be fine.
I use them in this way at work all the time.
However that is the least of your problems, the functionality of the MiniMig source (to be used for chip replacements) is more of an issue.