While I certainly wouldn't contest the theoretical aspect of whatever phase shift may or may not be present in the 6-channel bypass, I think there is a real world aspect to consider as well. How much does a phase shift actually impact the sound in that frequency range?

If you have two subs out of phase with each other, the problem ought to be obvious. You're going to have cancellation. But that isn't what's happening here as I understand it.

If the two subs are in-phase but out of phase with your "small" speakers, you might only have an audible impact in the form of some cancellation around the crossover point. And then the audible impact may be limited.

In fact, I saw some measurement graphs today comparing in- and out-of-phase sub performance and it was consistent with the guesstimate that I just mentioned. There was a little suck-out in the crossover range but nothing likely to be particularly noticeable in real world content (as opposed to pink noise test tones.)