The 060 had some features that would break backwards compatibility, even with the Amiga. The speed difference really wasn't worth the hassle.

Of course Apple knew about my Mac emualtions - I visited them in Curpertino, met Scully and a bunch of their engineers and marketing people when I was trying to get Apple to license us Mac ROMs for inclusion with the A4000/EMPLANT bundle that Commodore wanted. Of course Apple was not too thrilled to see their OS running faster on Amiga hardware than their own hardware. They cited concerns about compatibility (when we were actually more compatible than any single Mac) and denied the ROM license.

Just an update. I am not sure if the JIT version got BFFFO and other bitfield instruction support - but that's not optional for the Mac OS which uses these instructions like the Amiga uses ExecBase! :)

Which setting in WinUAE run Fusion the best? Which settings run FusionPPC the best?

Use 68040 with MMU, best compatibility with FUSION. I don't have a clue for FUSION-PPC