According to Jason and the service bulletins, as long as you use the proper chain files, you can mix-n-match EMI and non-EMI boards. I know I just loaded a PS/3 board set with the relay board (non-EMI) with an EMI tender board, runs fine.
This is the service bulletin that addresses that issue: service_bulletin_101017a
If you don't have the correct code, you can run into issues. I had this happen one time early on, the boiler board obviously was fighting itself and apparently turned on all the motor driver FETs at once. Fortunately, I had my bench magnetic circuit breaker enabled, and the breaker tripped immediately and didn't cook the board.