If you've checked the phase, just ignore it. Some speakers have tweeters intentionally wired out of phase and audessy could pick up on that. Audyssey does not determine crossover frequency, it simply reports the f3 to the receiver and it picks large or small, and the crossover frequency.
In the majority of circumstances, it best to have all of the low end routed to the sub, the sub can be optimally placed for the best low end response, whereas speakers cannot and the response is going to vary considerably throughout the room. This is not a rule however, in some rooms, I've found it get better response with lower crossover points.
You should definitely disable the LFE + Mains setting unless you want bloated bass and cancellations.
The other thing to consider is that forcing a single driver to cover multiple octaves introduces intermodulation distortion. If you play a 40hz tone and a 800hz tone at the same time with your speakers set to full range, raising and lowering the volume you may notice some warbling of the 800hz tone. Thats IM distortion. Ideally each driver should cover no more than 3 octaves. From 20hz to 80hz, that's about 3 octaves. Let the sub handle that.
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