Crossover frequency
Nice clarity on your test results.
As said by other, the Audyssey setup just gives you a good starting point, it is not hte ultimate answer. YOU, the listener can and should adjust to your tastes.
From you test (2) it sounds as if your front speakers cannot handle a 120 Hz frenquency or lower. From your test(1) , it sounds as if your front speakers can handle a frequency as low as 180 Hz.
So, your crossover should be set higher than 120 Hz and somewhere between 120 Hz and 180 Hz, since 180 Hz is okay.
From page 31 of your manual you can set the crossover frequency at the following values: 40, 60, 80, 90, 100, 110,120, 150, 200, 250.
If you can run a test tone of 150Hz and it sound sokay, then you can set the crossover at 150 Hz and I would do so

. If you cannot run a test tone or you can run a 150 Hz test tone and it sounds bad, then leave your crossover set at 200 Hz.
I am assuming

that your "Subwoofer: FOUR 4” Aluminized Fiberglass Matrix" can handle 200 Hz and below frequencies. I am not familiar with that subwoofer.