Sort of like how a PLC uses RLL that is based on electronics rather than assembly language or C++ that is based on logic instead?
If the Mega65 does bank switching, can you set up virtual 64K areas in the RAM with the 32 Bit register that jumps to it via bank switching? You could make one 64K area for C64, another for VIC-20, and a third for C16 and maybe a fourth for GEOS (I think if GEOS is added to a ROM and then loaded into memory from the ROM which can be reprogrammed as a EEPROM it could load the machine faster.)
A major selling point for this machine would be that you don't have to wait long for it to boot and load programs like some modern PCs do. It also does not take that long to be shut down either. Look at how long MacOS or Windows takes. Sometimes simple and smaller memory footprint is better.
Here is a VIC-20 and C64 memory map comparison:
Here is a C16/Plus4 memory map:
I do think the priority is getting the C65/C64 software working first.
Can all three machines use the GS4510 CPU and VIC-VI chip in Vic-II and Vic-III modes?