Something I discovered when working with SpectraLAB might be worth mentioning: Standing waves where the front and rear speaker soundwaves overlap. Hard to explain in words, but basically what I'm saying is that there will be peaks and valleys in the sampled frequency response, and those peaks and valleys will change depending on where you move the microphone in the car (forward or back). So there might be some merit to having an automated system average two separate passes, once with the fader cranked forward, and once with the fader cranked backward.

Unless you're talking about something different, this effect (nodes and antinodes at room modes) happens even with just two speakers, or even with just one. But it only happens with frequencies where one wave (a) fits in the car and (b) is quite large compared to the size of the human ear, so say 150-500Hz. All you can do about it is mount the SPL meter approximately where your head would be. Hopefully these effects aren't too severe, though; the inside of a car is a complex enough shape that I'd expect the room modes to have pretty low Q.

There might also be merit in averaging four (or two) runs, one for each occupant's head position.

Peter