As someone who has an expanded A4000 as my main "real" Amiga and as an owner of a FPGA Arcade, I expect the FPGA Arcade to replace my A4000 once I can get the daughterboard.
As a bare FPGA Aracde, it is really an expanded A1200 with a faster CPU, extra RAM, scan doubler, RTG and a PS2 mouse adapter (or USB mouse adapter).
Once the daughterboard is added, you can say that it has a 68060, even more RAM, another hard drive, sound card and a Deneb USB.
When I consider what it cost for me to put my A4000 into a tower, add a Warp Drive 68040 with extra RAM, FastATA4000, SD/FF, Deneb, Mediator for RTG, Spider USB and SB128 Sound, then I think the FPGA Arcade will be the cheaper option.
That said, I can't plug my Emplant card into the FPGA Arcade (but I could always run Shapeshifter I guess).