I think he is largely talking about the physical setup and checking all the speakers are working and you can get sound out. Yes, you are correct, Audyessy will change the speaker sizes, distances, levels, crossovers and Eq. However it might fail if the speakers are wired incorrectly or not present. After the setup you may want to go back in and adjust the speaker sizes, distances and run a level check with an external device like a phone or a tablet and see if they need tweaking.
The setups have a habit of setting things to large where as you will most likely want them small with a cross over point for Sub.