Technically, I don't really know how a pass through works, only conceptually and with no supporting evidence.
It's this line that sticks out in my mind

This meant that I could control the front/rear fading from the empeg, and the subwoofer level would simply be part of the rear speaker level.

This sounds like the Output line is passing through the signal from the Rear inputs. The signal coming from the empeg should be plugged in to the Rear input, then the Output line connected to the Front input.

If the amp was ANDing or RMSing or whatever, the inputs on both the Front and Back input of the amp, wouldn't you have a loop when you connect the output back into the Front Channel?

Please help me see this clearly.