Post Audyssey calibration appears slightly different but not better.
The steps to good bass are:
1. Best placement of subs in the room
2. Alignment of the subs to each other.
3. Alignment of the sub group/array to the mains.
This could be just a problem with #3 alone. You could use the REW RTA (real time analyzer) feature or take frequency sweep measurements while changing the sub distances equally for both subs fwd and/or backward in increments of 1 ft to see if the response smooths.out. If you should go past a point of max improvement then back up in smaller increments. You could also raise the XO to 90 and/or 100Hz to check that option. I recommend writing down your sub distances before starting so they can be put back. Turn off all soundfield processing (ex. dolby dsu, dts neural x, etc). Leave Audyssey on for this. It's my understanding that with Marantz after changing the distance you will need to back out of the change setting gui for it to actually be set. If you have no plans to move the subs and you do plan to use Audyssey going forward and you don't plan on adding new hardware such as a MiniDSP to manage the subs, this is your best choice.
Optionally, for a possibly better look at what's going on these measurements taken with
a) all soundfield processing off,
b) Audyssey off
c) a timing reference. Assuming a usb mic then it will be an
Acoustic Timing Reference.
d) Take the sub "full range" measurements by changing the fronts to small and and the XO to the highest setting possible and disconnecting either the right or left front and sending the signal to it.
e) a range 10Hz to 300Hz
Front Right Full Range
Front Left Full Range
Sub 1 Full Range
Sub 2 Rull Range
They should show if there are obvious opportunities in the current set up or the in-wall speakers themselves.