Yes, the test is between then LFE & the mains. BUT, you have to select a test track based on you crossover point. There are selections just like the 950 has for the digital crossover.....40,60,80,100 hz. I selected 80, and played it. It then sends an 80 hz tone, which, because its exactly at the crossover point, will come from BOTH the sub & the mains, making a phase test between the mains & sub possible. I don't think there is ANY signal on the LFE. I could check if you'd like by pulling that cable.
This weekend, I'm going to try to redo the test using a stereo PCM disc the way you are with stereo PCM coax vs stereo input via the 6 Ch Direct to see what happens.
I didn't know Chesky was into SACD! I have the DVD-A test disc and a DAD test disc (the DAD is the only DAD I have, and can't get the 950 to run it through DPL2...have another thread here on that).

Bosso- the 80hz filter IS there, or I wouldn't get any output on this phase test.