Huh - literally every trick in the toolbox (pun intended) is used to integrate the running System with the host OS.

An actual Quadra ROM, but a System Enabler (and a Helper application). For Toolbox UI services, it does everything from patch the Toolbox (e.g. to prevent windows from being moved onto the MAE toolbar) to call the host OS for services (eg direct translation from QuickDraw to Xlib.)

But so many other mysteries remain.

How is transparent disk access/conversion implemented if there are no SCSI devices, and the ATA/IDE Manager isn’t installed? Is the File Manager heavily patched as well?

Is the 68k emulator patched to map the graphics card DeclROMs into the memory windows the Slot Manager expects? (Why not just patch the Slot Manager as well?)