The rear speakers are run from a strictly conventional output from the HU. There's a small box near your back speakers which houses a small amplifier and the AFBS circuitry, and this circuitry receives signals from small microphones implanted into the rear speakers. The signal is adjusted at the amp and sent back to the speakers with no input from the HU at all. This means that you can get an aftermarket HU and still keep AFBS functional, but not aftermarket rear speakers (unless you figured out how to swap in the microphones on your new speakers).
Incidentally, my largest gain in SQ came from swapping in a new HU. If you consider buying even a cheapo alpine unit, you can bypass the AFBS/amp and run 4ohm speakers in the rear, which will open up a large range of speakers. Personally, I'd be surprised if I could pick out the difference between AFBS-modified and straight-through sound, although I'm not really an audiophile either. Hell, I've got my rears disconnected entirely

I would guess that the SQ increase from going to an aftermarket HU & rears would far outstrip any gains you're seeing from AFBS.