A/UX boots macOS, then loads a loader app that takes over the machine and boots the kernel. The emulator Shoebill “cheats” and reads the kernel from the UFS disk directly and jumps to that.
That was always really funny to me. Your machine boots MacOS, presumably because it was easier to let it deal with hardware initialization than to rewrite it, then hands control over to A/UX which promptly runs MacOS as a Unix process. Which you can kill.
Oberlin College had a Workgroup Server 95, basically a repurposed Quadra 950, running as an AppleShare file server for a significant number of users. That was how Apple was marketing these things, and thinking about it - use our Unix to serve your MacOS boxes! But we have no real interest in Unix, just buy more MacOS boxes! See: Apple Network Server.
I remember my father mentioning talking to someone from Apple at a USENIX, probably late '80s or very early '90s, and them admitting that A/UX was essentially a glorified public beta. That might have been in the A/UX 1.0 or 2.0 timeframe but it says a lot about the sorts of resources Apple was dedicating to the idea.
-Henry