This is one of the things Audyssey corrects.
It is not unusual to read posts where people ask why Audyssey sets the distance incorrectly from the sub to their listening position. It is for phase matching.
Audyssey generates a signal, then measures how long it takes for that signal to reach the microphone. This time, along with the signal wavelength, can be used to determine phase.
If the phase is at or near 180deg out, it will tell you a speaker is miswired. If a speaker or sub is just a few degrees off, it can fix it for you. By delaying the signal to the speaker/sub, it can effectively change the apparent distance between the speaker/sub and you, thus changing the phase.
So if you use Audyssey correctly, and don't manually change the speaker/sub distances it sets, you don't have to worry about "out of phase" with your speakers or sub.