No, I think that we actually do agree. If you notice in one of my earlier posts, I have my crossovers set as you describe above (60Hz for the mains for example). My point was that just setting a speaker to "large" usually means sending the full band of audio to the speaker, which is almost always a problem unless you really do have some great speakers. That is different than setting crossovers to specific frequencies.
With my 805 (I assume this applies to many others), Audyssey set my two front speakers and my two surrounds to "large" not a specific frequency. A setting of large would almost for sure have been outside of Audyssey's EQ work. However, with the 805, there is no way to tell what the real crossover frequency Audyssey is recommending. The 805 just said large. If I had not went back and adjusted the crossoevers to 60Hz, all four channels would have been receiving full band audio, which none of my speakers are cabable of.
The problem with most AVRs is that they take the frequency response data from Audyssey and it decides how to set the speaker. Any user, and especially new HT fans, should be very careful when they setup their system. Just do not let Audyssey, or more correctly the AVR, just set the crossovers without checking them.
I just noticed that you have an 906. Did Audyssey set all your speakers to specific crossover frequencies? If yes, then that is probably why you thought that I was saying something different than what I actually did.