Interesting, I'm wondering if there's an interrupt somewhere on the SE's PDS that a processor card can yank on and hold onto right from the get go in order to disable the 68000 on the MoBo without need of a driver?

edit: just noticed, there's no MMU or provision for one on your board. Can the SE address 8MB without using Compact Virtual? My PowerBook_100 did and the Portable addressed 9MB without one if memory serves.

What's the memory config for your system?