IIRC, there was another computer idea floated around in Apple based on the 65816 that was killed before the IIgs project was started.
Making a faster Apple II would eat away Mac sales without providing a path to evolve. That’s also why the IIgs was never allowed to have the higher clocks the 65816 could use.
The path for the 68000 was much clearer - it already starts from a clean 32-bit architecture with a 16-bit data bus and a 24-bit address bus. The 68000 and its offspring also powered multiple Unix workstations at the same period, creating a critical mass of development tools that didn't exist for the 65816. It went on to 32-bit data and address buses, FPU, MMU and extra instructions and survived for some time after Apple, IBM and Motorola mostly gave up on it and went on with the PowerPC. All in all, the 68K architecture carried the Mac line for more than 10 years.
That would be very unlikely to be possible with Apple II software compatibility. In this case, the PDS Apple II board was probably the best option for Apple. It could have been designed to have a version of GS/OS using the Mac an an IO device in a software-friendly way, but the GS/OS software base was not there to justify the extra effort.
Based on the Commodore 128 64 mode it is backwards compatible. The Mega 65 is the fastest 8 bit computer out there.
The C65 would have been a much nicer computer than the C128.
Unfortunately, for Apple II users, the fact it doesn't match 6502 timings perfectly makes it difficult to use as a drop-in replacement, as time-critical ops in joystick sensing and floppy IO may need some adjustment.
The Commodore 64 has a 65816 Super CPU add on that some games can take advantage of. It is needed for that Super Mario Brothers clone to get proper scrolling.
Apple went on to use the '816 in the Apple IIgs, though.