PH, yes, those numbers all seem very reasonable, reflecting the capabilities of the speakers in your room environment. Nevertheless, I'd suggest manually resetting the M22 and M2 crossovers to 80Hz, to take a little more of the bass load off them and put it onto the sub, which handles it better.
The -6dB sub result isn't a problem, but if you re-run Audyssey you might start off with the sub volume control(it isn't a gain control, audio amplifiers have fixed gain)at 4 rather than 6 so that the net result is closer to 0. No, if you want to run the sub a few dB "hot"(but keep in mind that a correctly calibrated sub level shouldn't have the sub loud enough to draw attention to itself), it doesn't matter much which volume control that you turn up, although it isn't a good idea to have the control set near the max.
