Is it really a big deal? OK, there's a subtle difference in positions 2 and 4 of a Strat set with an RW/RP middle.
But an HSH set? It's not as if there's a "classic HSH positions 2 and 4 sound" we've all grown up hearing in our heads.
If they turn out to be out of phase, then swapping a couple of wires will fix it. Beyond that, I defy anyone to notice anything "different" about the sound.