My best guess, having attempted AutoEQ setup multiple times over the years with several HU models. Haven't used it lately so my recollection may be a bit lacking... others will likely correct or state their opinions to the contrary 
Setup automatically bypasses any EQ settings, but not crossover settings... the latter of which it will change as it determines appropriate. However, crossover frequency and slope always seems to be changed to, if not already there, 80Hz@-6dB per octave on all 5 channels. Output level (and subwoofer polarity) may also be change... automatically.
When AutoEQ is enabled, any applied EQ levels are invoked behind the GUI (i.e. not displayed)... so user settings are applied as an additional layer. Crossover setting are as shown in the GUI, but changing to any other settings with AutoEQ enabled essentially defeats its purpose.
FWIW, I have never attained results satisfactory to my ears and consider implementation to be a waste of time. I have not tried using any microphone other than the one included with older models. If/when I get my 8000 installed, I will likely try it again with the specified mic and a 3rd-party calibrated microphone... and after each run a spectrum analysis using 3rd-party software and the same 3rd-party calibrated mic, just for comparison.