Audyssey does not have the final word on xover settings, your receiver does, but that said, leave them be. It is just about certain that Audyssey found your F3 points to be that high on your current speakers; if you lower xover, these lower frequencies will not have been accounted for during EQ, simply because the software sees that your speakers have no business trying to play that low.
The phase, don't worry about it for now, Audyssey should have taken care of that. If you didn't have Audyssey, you can have a friend play with the dial while you're seated, and the better setting will sound more full. Obviously, use bass heavy material.
LPF you can leave at highest setting. It doesn't really matter for a huge proportion of what is made for it, at least as far as my understanding or impression. However, once in a while a movie will actually send LFE info that does get significantly above 80hz, and so you'll get some in that case.
So you're now wondering, well but my xover is at 80hz, how or why could it matter? You then have to understand that "xovers are not brick walls". Hope that helps.