Putting the power lines underneath the 68k is clever. I had never thought of doing that before.
As for EEPROM vs NVRAM, if you have an EPROM programmer, there isn't any effort required to program the ROM, and NVRAM is just more expensive compared to ROM.
Also, what is your general plan for the design? Is it to have multiple CPUs running simultaneously, or will only one CPU execute code at a time? In addition, will they be sharing a bus, or doing some mailbox message passing?