Me too, but whether you make the adjustment on the App or later on the AVR should make no difference. For settings such as DEQ, the App sends the instructions, the AVR executes it, as simple as that.
If the AVR wouldn't execute certain things set with the App, then it would be because not all the information get sent due to certain network issues, bugs, or something else. That happened to me a few times, such as missing the "flat" choice, it always got fixed after re-sending the file. I asked Audyssey about it, and that's what they suggested, that is, if and when it happens, just send the file again, and again if required until it gets fixed.
I lost count how many times I ran Audyssey, with or without the App so I am very confident that is the case. If someone can link that video I would like to see, for now I suspect it might have been taken out of context, unintentional of course.