While automatic room EQing is often improving the sound, it can't do wonders - and very often there is room left for further improvement.
Example: The crossover frequency is a crucially important frequency sitting at a point in the spectrum where much of the energy is concentrated in music (60-80 Hz). Getting the xover wrong, for example creating a dip due to cancellations, obviously can have a huge impact on the perceived sound (with identical speakers losing punch of the kickdrum when playing back stereo mixes over the center speaker could be one example).
Let's assume the software suggested a certain xover frequency for the center.
You listen but are not really satisfied and try different settings.
So among the xover settings you will find one you like most.
But what do you really know?
Was it really a certain xover that reduced the problem? What if a different parameter, for example the sub's distance setting, is causing the cancellations? By measuring you would see if the problem persists, but by ear you could be tricked to believe you have found the optimum.
To how many mixes have you listened to to check the setting? 10? 20? 50?
And what kind of mixes did you choose as reference?
Only music you like? All genres? What genres?
Why do music studios have not speakers for different kinds of genres of music? Because they aim to play back as flat as possible. That's the good guidance to judge any kind of mix/music.
So when you have reached the 20th reference mix during testing, do you exactly remember, how the kickdrum in the second song sounded and how it compares to the current one playing? Ofcourse not.
The truth is a layman cannot judge sound quality by listening.
Even only very few professionals are able to do so when it comes to room acoustics and sound system tuning. There's a reason why professionals use analyzers all the time to help their ears...
What complicates things even more: mixes sound waaay too different to be able to judge the sound of a system by listening to only a few of them.
On one mix the kickdrum makes you believe you have finally found a very good and neutral setting, while on another mix the bassdrum suddenly is lacking power and has too much subbass.
What's correct? What's the better sounding mix and what is just sounding better on your system in your specific room because of the tremendous coloration and filtering that is going on in every room?
Chances are VERY high that it's your monitoring that emphasizes certain aspects of a certain mix that makes you like one mix more than another.
The only thing you can do by ear is to say, if you like a certain mix/sound more than another on your system in your specific room
. But which one actually really sounds better? That can only be judged on optimized systems without huge problems in nicely sounding rooms. Everything else is hogwash.