Well, my dense understanding is that once the speaker calibration is done via the AVR, then the resulting info is processed and something is spit out and that becomes the default for the audio output throughout whatever HT system one might have. I suppose that the speaker calibration is somewhat primitive but it should take into account the speaker distances from the microphone and set appropriate delays, one way or another. It also sets whether the speakers are designated small or large, depending upon the output of the subwoofer, as well as the crossover for the subwoofer. There is always the possibility that the calibration system just gets confused. For the present, I have just accepted the calibration when it came to setting the speakers. Whenever I get back my main front speakers from repair, I can start to play around with this stuff in earnest. It is somewhat humorous to encounter these sorts of problems after setting up the HT system 18 months ago. For me, it turns out to be continual tweaking as well as upgrading components. That is the path and I have learned a lot along the way. Then there is always the continual thought of how I can improve it and not break the bank. That is the challenge and the fun of setting up a home theater system.
Anyway, I don't exactly understand what you are getting at when you write not to have anything turned on. If you are referring to the calibration procedure, then the only thing that is on is the AVR and the powered subwoofer. Everything else is electrically off.