I'm curious if Amiga UNIX can be made to work on the MMU-patched UAE. I'm a little skeptical as the patch documentation (which is pretty sketchy) targets running Linux, and the one significant website I've found talking about AMIX assumes you need real hardware. But I don't know much about Amiga, so... might be worth a try.
(I've never futzed much with UAE simply because I don't have any nostalgia for the Amiga. Thus I don't know how exactly-specifically it can be configured to emulate a particular model and how the MMU patch interacts with that.)
The Atari emulator Aranym has the MMU support better integrated into it but it likewise targets Linux, most possibly because the Unix that was briefly bundled with a particular model of the TT030 is essentially vaporware. (If anyone on the planet has a working TT030 UNIX system it might be interesting to see if it has any binary compatibility with A/UX.) The only 680x0 emulator I *know*, as in having tried it, that runs a commercial MMU-dependent UNIX is TME, the Sun3 emulator. But of course that would be a given since a Sun emulator that didn't run SunOS would be by definition pointless.
(There may well be working emulators for even more obscure UNIX workstations that I don't know about. As an amusing side note M.E.S.S. has added a skeleton driver for NeXT systems. Don't hold your breath for that one...)