As
@lovinthehd said above, nothing gets tuned or detuned during calibration. The equalization (EQ) part of the calibration software is not meant to correct the frequency response coming out of a speaker. It does try to deal with the sound once it has emerged from the speakers as it reflects off nearby walls, floor & ceiling. It's a complex process and a lot of people mistakenly assume the EQ can correct a speaker's output. It is mean to equalize the room & speaker combined.
When you adjust the volume level of each speaker with those test tones, you are simply adjusting their volumes relative to each other. You also adjust their sound's arrival times for someone sitting in a central listening position.
Sound travels through the air at roughly 1,000 feet per second. We can hear differences of 1 millisecond or about 1 foot. The goal is set each speaker's as loud as the others, and to have their sounds all arrive for a listener at the same time.
The AVR manufacturer can't know what speakers you have or where you've placed them. The AVR does come with default settings that will probably not work well for you. Since this is all digitally controlled, you have to set this yourself using that calibration software. Before the calibration software existed, all this had to be done manually with a sound meter. Most people never bothered.
I hope that helps.