sorry for not being clear, what i meant was reflections due to room, might cause cancelation or addition of bass at different parts of the room. and the mic might be reading wrong input, hence replacing the mic can give u slightly different results.
the crossover for the subwoofer can be set in amplifier, but YPAO should do it for u, it should identify ur sattelite speakers as "small" and based on their bass response, set an appropriate crossover frequency.
if YPAO sets ur main 5 speakers fine, but fails to set ur Subwoofer, u can accept the suggested settings and then manually retune the subwoofer