I'm sorry that XT-32 seems to be introducing a big dip at about 40Hz, and I can't account for it. XT-32 has 4096 control points (taps) available to the .1 channel, though, which allows for fairly precise adjustments to the frequency response. I am having a hard time believing that Audyssey aimed at 50Hz and hit 40Hz instead. But, I don't have another explanation to suggest.
Presumably your subs are already in the best positions you can put them before Audyssey attempts to EQ the response? I ask because I see a lot of peaks and valleys above 50Hz, both with and without Audyssey. Room treatments certainly help, but below about 120Hz it takes fairly thick bass traps, and perhaps a lot of them, to have a very significant effect on the FR.
To your point of just leaving Audyssey off, though, I think that is always an option with any version of Audyssey. Measurements notwithstanding, I think that our ears need to be the final judge of what Audyssey is doing. For instance, I have fairly extensive bass trapping (among other treatments) in my large room. The good news is that I have excellent bass reinforcement and low frequency containment in the room. The bad news is that the irregular geometry in the room creates a lot of peaks and dips which I just can't tame without room correction.
The other day, I decided to experiment with some things again, and tried turning XT-32 off for the first time in a while. My bass below about 80Hz or 100Hz sounded very occluded without Audyssey. After becoming used to a clearer sound, that boomier sound is just unlistenable to me. Irrespective of other portions of the frequency range (and Audyssey also helps with my mid-range frequencies, and doesn't adversely affect my treble) I would use Audyssey solely for the mid-bass frequencies and below.
But, that is the bottom line for me. If you can't hear a difference with Audyssey on, then it doesn't matter whether it's on or not. If the sound is definitely better with it off, and you are convinced that you can't improve it with further experimentation, then just leave Audyssey off.
I wish I could offer some additional trouble-shooting suggestions, but other than initial subwoofer placement, I can't think of any.