Nothing to add except some questions.
It appears that a lot of settings(balance,bass,treble,auto volume,etc.)need to be set at their respective neutral position in order to prevent bad things from happening.(clicks,pops,blown speakers)
Would it be possible to boot the player in a "safe mode" with these controls at their neutral position?And then do the autoEQ.Or do it in Hijack?For instance.."if microphone 1 then set all controls to neutral"type of config.