Maybe it makes sense to sum up the difference:
CPU
in FPGA ~ 600 Mhz 68020 Speed
in Very Good FPGA ~ 1200 Mhz 68020 Speed
+ needed investment to develop an FPGA system is low - some hundred to maybe thousand $ to get prototype
+ Bugs can be fixed in the field
The biggest advantage I can see is that it would make it easier to support different MMU types and switch between them. An R4000 style MMU where the CPU does the page walking could be added for those that want it, or an 030/040/060 MMU could be used by those who wanted to be compatible with old software.
I personally only want an FPGA that runs code that requires an 060 CPU/FPU/MMU. For me any other instructions or functionality is a big negative. It would be awesome if someone could do 040/030/020/010 & 000 implementations too. If it's not this project then hopefully some day someone will do it.