Phil, you are absolutely correct about the MCU differences. The early hardware used a 68705, and later games (mostly 3D ones with analog controls) used the M37450 which is a 6502 variant with more instructions.
The C68 MCU has a pin to select internal or external ROM that is brought out to a jumper on the motherboard. The pin is latched internally during a reset pulse so subsequent changes are ignored. Just to be sure I verified with a trojan that the pin state really is ignored after a reset.
I also tried various out-of-spec reset pulses, and changing the external memory map in hopes that it might crash. No such luck.
Some games like Suzuka 8 Hours will use the C68's internal ROM and have no external ROM. Others like Final Lap 3use the external ROM exclusively. I feel certain the internal ROM contents are the same for all boards that use the chip.
I sent a C68 to Guru for decapping, it's definitely on the list.