Yes Indeed. After taking a real quick glance at your manual, it seems that they have combined both the basic speaker setup (distances and levels) with the EQ and crossover adjustments.
In my older model, it was a two step process. It began with the usual basic test tones, set the distance & levels and then it would stop and ask you if you wanted to continue on and do the auto EQ portion. Your model seems to take an 'all in one approach' from what I read.
If you want to experiment with not using the Aut0-EQ, then I would suggest turning off Audyssey EQ altogether and double checking the speaker distance and redo the level checks with an SPL meter. By turning it off, you still retain all the settings it came up with so you can go back to compare without having to run it again. Turning it Off is described on Page 43 of the manual.
