I am confused. Are you saying you reversed the polarity on one driver in one speaker, and it didn't make any difference on the polarity test? It sounds like you are making this too difficult. If you have the speakers open, I think you should verify that all drivers are wired with the correct polarity, and re-run the Audyssey calibration. If Audyssey reports a speaker out of phase, ignore the warning and proceed with the calibration.
I currently have the midranges wired in reverse. Audyssey reports an error on both left and right main speakers (which it probably should, since one of the drivers is wired out of phase) but the Farr test sounds correct.