Yeah, I guess improved performance and perfect compatibility are kind of mutually exclusive, due to the need to maintain exact timings and so on. I wouldn't mind a "Turbo" Amiga core for the MiST, with all stops removed, for those few demanding 3D games etc., but that's why I'm interested in the Vampire V4 as a complement to my MiST.
Compatibility has very little to do with timing. If a program is tied to the timing of a CPU, then it's going to have a bad time running on any accelerator. If it's written to use the Amiga's timers, then exact timings in an FPGA are unnecessary.
Only very poorly written software would be affected, so you'd probably boot off of the m68020 for those. Or, as you wrote, having a "compatible" slow mode and a normal, fast mode would be a good thing.