I have the same feelings, and have gone around in circles in my head a few times on this. But from a practical standpoint, the 68000 is the only part that can be readily sourced today. The IWM, VIA, SCC, PALs, and other goodness need their behaviors reimplemented in an FPGA (or maybe a large CPLD). I suppose you could put each one in a separate FPGA so you could label them, but I'm not that masochistic.
It would be cool to use a real 68000, but I've worked through the details and it would increase the necessary FPGA pin count to where I'd likely need two FPGAs, or a whole bunch of extra muxes and bus drivers, so it complicates things. The soft-CPU also makes it a lot easier to debug during initial development.I'm going to continue with the soft-CPU for now, since it's already there, but may switch back to a real 68000 later once everything is more or less working. There's still lots of room for Mac-specific hardware goodies when I get to building a custom board too. Maybe add connectors for vintage keyboard, mouse, serial, and even floppy if I can find a source for DB-19's!
It's actually not a JITter, but a full-fledged 68000 realized from the "sea of gates" of the FPGA. So there's no emulation or dynamic recompliation involved. It's basically exactly the same as having a real 68000, just internal to the FPGA.