I'm impressed Squidly, you did your homework!
I actually didn't even think about that LOL. So with the 3-way front, having the sub connected to the low outputs, you can keep the polarity of the sub the same as the underseats.
Having said that, it is still good to experiment. In my car, for example, I'm running a 3-way active front, and despite auto-T/A, I had to put the left tweeter in reverse polarity for it to sound good. In the end, your ears are the ultimate judge, not the algorithm in the processor.
