I'm missing something here. The defintion of a crossover is that it high passes the mains (center, surrounds, and rear(s)), and low passes the sub.

Any time alignment should happen *after* the summing and crossing over. (That just makes engineering sense.) (The 5.1 analog inputs are a difderent story.)

I have spent a nontrivial amount of time making sure with discrete tones that my mains are in phase with my sub.

Am I missing something here?