Dan, since I saw this thread still going, my curiosity finally led me to look at the 6080 manual, since I had the impression(recently I've paid much more attention to Denon and Onkyo models, primarily because of Audyssey)that on at least some Yamaha models YPAO would set each channel crossover individually, even if the manual setting had to be one frequency for all.
Checking the manual, the setting when done manually does use that frequency for "all the speakers set to "SML""(p.74), but in describing what the YPAO calibration(not room equalization)did , it states under "Speaker Size" that it: "Checks the frequency response of each speaker and sets the appropriate low-frequency crossover for each channel"(p.29). Because of that statement, the question would be what does the display actually indicate as to the different channels when YPAO sets the crossover.
If still necessary, I'd suggest manually setting a uniform 80Hz as a compromise, and not using the "Both" subwoofer setting.
