I have Audyssey room correction set at 500 Hz and below. It really should only be used for bass correction, or one can get anamolies like you’ve noted.Two notes on Audyssey for me:
1) It destroys the high end for my setup. Makes a mess of my Paradigm tweeters. It works a whole lot better if I filter Audyssey from working on frequencies over 1.5Khz.
2) It is pure bliss for my subs. Before Audyssey MultiEQ XT32, I constantly futzed with levels for my dual subs. What sounded right for one source just was not right for another.
Since implementing Audyssey it's set and forget, the lows and mids all sounds great and never a futz anymore.
I love Audyssey, but know it's limitations.
YMMV.
I recommend spending the $21 (or so) for the app to do room correction.