Your installer guy is right about the time alignment sending an out-of-phase signal to the sub. That's all that the time alignment feature does, it delays one channel so that it's slightly out of phase.
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.
Since there are only two audio channels that can be worked with by the kernel or the player software, then it can't separate it to have the fronts do something different from the rears.
The only things that you can do differently between the fronts and the rears are the things already built-in to the DSP, i.e., the fader and EQ features.
All is not lost, though.
Despite what your installer guy said, it might not be that big of a deal. The *only* thing that having the left and rights being out of phase does is reduce the volume of the bass. The worst thing you'll need to do is turn up the subwoofer a bit louder, and maybe readjust the subwoofer volume each time you readjust the phase. And you might not even need to do any of the above. I say, just try it: Listen to some music and alter the time alignment. If you notice the subwoofer volume seeming to decrease, then you're hearing the thing your installer warned you about. But you might not hear any change at all, the phase difference might be quite small.
The truth is that the thing I just said happens anyway, with any audio signal, with or without electronic phase modification. As you change your position relative to a pair of stereo speakers, you're getting the same thing.
There will be "nodes" in any stereo pairing where you'll be at the opposite phase for any given frequency. It's most noticeable in the bass frequencies, of course... Once I had accidentally mis-wired one of my two rear speakers in the car and wondered why the bass response sucked back there. As I moved left and right in the back seat, I could hear the bass getting louder as I moved to each side. After I fixed the wiring, then the bass was louder in the middle and softer on either side. So it was six of one half dozen of the other.
For that matter, the subwoofer gets out-of-phase signals all the time anyway. All music recorded in stereo is a constant stream of out-of-phase signals. It's (partially) those differences in phase that make us perceive a 3D image at all.
So just try it, it might not be as bad as you're worrying about.