So those are mains (L+R)+Suboofer(s),but what did you set the XO to? Did you try plotting it using higher XO, such as 90 Hz?
It looks to me your mains and subs have usage output bu may not be capable to output much more than 95 dB from you main mic position. That's why I suggested you try running REW at lower level, say 75 to 85 dB to see if the response would become flatter.
You can see that Audyssey did improve things though, even in bypass.
The dip that you are seeing at near and below 20 Hz may not be due to the App roll off, unless you are still missing the latest update. It could simply be, as I mentioned earlier, the speakers and sub(s) have reached their limit. Audyssey can give it a boost (not much if due to room mode) but is limited to 9 dB maximum and if you compare the red and the blue, it does look Audyssey has given it the best it could do already.
Below are screenshots of my App's subwoofer EQ before and after the update that removed the 20 Hz roll off.
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