The Toolbox ROMs, right? I can see the utility of using that (I mean, beyond that you might need to use it to boot), but why couldn't A/UX call those APIs itself? I can easily see where bootstrapping through Mac OS would be easier, but I can't immediately see why it would be particularly necessary.

It's been a long time, but I'm pretty sure A/UX didn't use any of the toolbox roms and had it's own drivers (we had the source). A/UX booted from a MacOS partition because the Mac bootloader only understood booting MacOS (and it wasn't writeable with new boot code), so you booted to MacOS, then started SASH, which loaded Unix.