I'm reasonably sure that what you're asking for can't be done with the current empeg hardware. Here's the reason:
1. The MP3 gets decoded into two channel (left and right) wave audio.
2. That wave audio is then sent to the DSP, which is an ordinary off-the-shelf car stereo DSP, so it has only two inputs (left and right).
3. The DSP is what controls the front/rear balance and the equalization, and then sends the audio to the outputs.
I'm pretty sure that the time alignment trick is done by the kernel between steps 1 and 2. It simply delays one of the two audio channels slightly.
I wrote the time alignment stuff initially and Tony's right. Mark did re-write some of it for speed, but I'm sure he didn't change the concept - there really is no way with the current hardware.