Below about 200 hz, the room is firmly in control of bass. A 20 hz wave is 56.5 feet in diameter, so your room boundaries will determine what you hear and what you can't as very few homes can allow bass waves to fully propagate, thus creating room modes/standing waves. Audyssey does not in any way account for this.
But there is hope! We can try working with the minimal EQ built in to the receiver and hope its band presets line up with your room modes.
Room Mode Predictions - (predictions because walls have windows and doors allowing flex, lowering the actual resonant frequency from predicted)
1130 fps (speed of sound @ sea level) / room dimension in feet = modal frequency
With acoustic measurements (1/24 octave ONLY for bass) you can confirm these predictions and get the actual resonant frequency - the center of a peak/null.
You then apply an EQ filter with that frequency, adding/subtracting amplitude to bring that modal frequency closer to the relative loudness (dB) of everything else.
Q= bandwidth, so however many hertz-wide that peak/null is, is your Q. These 3 parameters create a filter.
Your receiver may be able to aid with this, but you may have to buy a minidsp 2x4 to implement all of the filters needed. I too have an open living room and calculated 15 room modes.
As you can see, this is a bit of a rabbit hole. Hence why these 'auto setup' programs are so popular, but unfortunately most are not advanced enough to truly be automatic, as your are experiencing. But realize that a few hours of work gets you the best performance out of your setup for minimal extra cost (minidsp + mic = $180).
The choice is yours to get the best Audyssey will allow, the best your own work will allow, or pay a professional. Welcome to a market still dominated by advertising, and not by science!