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.
...to a different extent at different frequencies, though, right?
There will be "nodes" in any stereo pairing where you'll be at the opposite phase for any given frequency.
But, especially inside a complex shape such as a car, reflected sounds and so on mean that nodes aren't very sharply defined: the bass got softer in the middle of your back seat, it didn't disappear altogether. With misaligned phase going to the subwoofer, certain frequencies (the ones whose wavelengths are half-integer multiples of the path difference) will be at zero volume throughout the car. For instance, if your channel delay is 4ms, corresponding to about 5ft of sound path difference, then your subwoofer's frequency response acquires utter dropouts at 125Hz, 375Hz, 625Hz, and so on.
Or is the answer that in practice these dropout frequencies are so high that they aren't being emitted by a subwoofer to start with?
Peter