Did you actually try to boot with anything less than 6.0.4? I need to make some pre 0.4 boot disks in order to experiment myself. I would think they should be installed for use with a SE. My understanding was that the Portable ROM included all the ROM patches made to the SE in addition to the new Power Manager stuff.
I tried to boot up with System 3.2 which got me the happy Mac then turned sad, before the System file loaded, so there was no basic hardware issues. However, I would think System 4.x on should work given that it supported SE resources. If not, I would think there is some way to trick an earlier system into running on the 100 as it seems to be mainly a software limitation in order to support some power manager features which are irrelevant if plugged into a power supply.
I wonder if the Portable would run an earlier system given that Apple's Gestalt ID system was not fully developed in 89. Anybody with one wanna give it a shot?