You have a point... The signal to the subwoofer would be precisely out of phase in a very pure fashion, so the nodes would be very sharply defined. But only on purely mono material and only in those sharply defined frequency bands. I suppose most bass guitars and kick drums are going to fall into that "pure mono" category, so perhaps it will be an actual issue, then.

If that turns out to be the case, I say just set the time alignment to zero and be a cowboy about it. Most folks' car stereos don't even have the time alignment feature; they just live with slightly-out-of-phase front speakers "AND THEY LIKED IT!"