Good point. Normally, should be no need to mix binaries, and the panel driver is the only thing that needs special settings. I'm looking at that currently, no reason it should other than it is very compute intensive and also scans the state of the lights the pdp1-emulator sets every 3 microseconds. Given that the original bulbs took tens of milliseconds to turn on and off, seems excessive. It appears to do this to accumulate a duty cycle for each light. Why that isn't done in the emulator itself is a mystery. Stay tuned on that one.
As for mixing binaries, the new display, t30dpy, is the only new closely-tied bit that will work completely with either version, and I think with various simh versions.
The am1 assembler is totally independent, but the debugger is totally dependent, won't work at all with the original emulator. The current modified panel supports the H.S. Cycle light, but that isn't used in the original. None of the new audio features or any of the added peripherals will work, no support for the IOTs, and neither will some of the extended 1D instructions.
Bill