I think it really is a point of "philosophy". If the result of electronic room correction is an acoustic that couldn't physically exist, then do our brains find it confusing? I just prefer to live with whatever the room does so that I don't have to worry about that question.
I do not understand the concept of "an acoustic that couldn't physically exist". Each room is different as to physical dimensions, materials, furnishings, etc., so there are an infinite number of possible resulting room acoustic signatures. The identical speaker system will sound differently in each of those different rooms. I think we agree on that. It is also possible by speaker or listener placement or passive treatments to alter that characteristic room acoustic at the listening chair. Your own room may be unique and special to you because of long familiarity with its acoustic signature. But, a more idealized room signature can exist "physically" somewhere, and there is a likelihood that an improved room signature might be preferred by most listeners.
Your philosophical objection seems to be to using active, mike calibrated DSP EQ filters to change the room acoustic via controlled, specific alterations to the output from the speakers to compensate for frequency and other room-induced abberations, which can be shown by measurement to physically exist at your ears in the room. But, what if (a.) it could be shown that the net perceived result at your ears via that means was no different from some other untreated room, without the application of EQ or a more idealized acoustically treated room? What if (b.), it could also be shown that the insertion of DSP EQ into the signal path was transparent and imperceptible when all EQ filtering is turned off?
Philosophically, we differ, which is fine. I believe from experience in a number of different rooms with a number of different speakers and DSP EQ systems, the answers to (a.) and (b.) are it most definitely can be shown. You, for whatever reasons, do not agree, and you believe that the result must be "confusing" to the brain. I have found no one yet among the listeners I know who agree with you. Ok, I am not writing a scientific paper, nor are you. My sample is anecdotal based on sighted A-B comparisons, and it is in the 10's, not hundreds or thousands of listeners. But, I know of no one who has the room EQ capability in their system who regularly turns it off because they think it sounds confusing or more implausible. They all think it sounds much "better".
You are perfectly free in your philosophy to disagree with audio science, as representated in many papers and commentaries at this forum. But, I believe if you see a, say, +10 dB narrow peak (I have measured worse) or a similar dip at one or more frequencies with your speakers in your room, it is a problem that will not go away. That is a big, readily audible frequency response issue that can be caused by the room with even great, anechoically "perfect"speaker response. In my philosophy, now that we have good tools to deal with it, such an issue is more disturbing to listening pleasure than trying to ignore or deny it.