Yes, that is how it was for me as well. SW plays the tone at a lower frequency yet at the same volume, that is a trick by our ears I believe.
Here's my latest measurement data. I have a X3800H, but that should not matter.
Speakers: 5.1.0 with fronts: Proac Responce 1SCs, center: Proac Response CC, and surrounds: Proac Tablet 50s. SW is SVS Micro 3000.
Audyssey put all crossovers at 40Hz. I have Preset1 as original ("for music"), Preset2 with crossovers at 80Hz ("for movies"). Or that was the plan. I almost never switch off from Preset2, I've found out.
I use DEQ, as it works for me, also because my listening volumes varies.
My latest tinkering was to up the SW level by +1.5dB. Before that, I was often tinkering the SVS app upping the level there by 2dB. I found out, and I don't know why, that doing this via Audyssey setting works better. For my ears, at least.
Finally, regarding the DEQ settings, what I've understood is the key setting to consider together with DEQ is the Reference Level Offset. Roland Sotay in his Secrets of Audyssey book(et) explains, that Audyssey increases surround volume levels by 1dB for every 5dB reduction in volume from reference level 0.
Therefore, listening at -20(dB from 85dB) and with Reference Level Offset at 5 final correction would be -20 + 5 = -15, and surround compensation thus 15/5 = 3dB.
Initially I did compensate this feature by lowering the surround levels with -1.5dB which seemed to work best, but lately I haven't done that. Either I've become used to surround levels varying a bit, or perhaps, my wife's become used to for me to playing streaming content (TV; movies) louder
I have kept RLO at 0, despite the recommendation to try 5 for movies and 10 as the RLO for TV and music content. This could be done at per input I understand, but I haven't bothered, for I am at least for now quite happy how everything comes together.