I have the 47ai set up with the bass management off, in other words, all speakers set to large. That's the only way To do it, since the 950's bass summation is always on.

I went back and re-read your post, and got just the opposite results! I am usinging a Chesky DVD-Audio Test Disc, that has both DVD-Audio & Dolby Digital tracks. They have tests that give tones at your selected crossover frequency (I used the 80hz one) that say " in phase...out of phase". The
DVD-A track (6 channel analog in) has the first track (in phase) louder than the second one (out of phase).
I then switch to the DVD optical input, switch the DVD player from DVD-A to DVD-Video (done in an internal menu option, The 950 says Dolby D 3/2.1. I play the SAME test band for 80 hz., and again the first tone (in phase) is louder.
I don't understand why yours is out of phase.
Maybe the DD decoder (which you aren't using in your test) adds a stage of inversion?
However I'm glad I don't, because my sub has no phase reverse switch!