The funny thing is that to begin with, depending on the overhead mic setup, the bottom mic may need to be polarity reversed just because of that. Not as much of an issue, usually though.
But then there are snares where, upon being hit, the bottom skin actually gets sucked in/upwards and thus the "polarity" of the air push/pull is already reversed going into the bottom mic. If you flip the polarity of the bottom mic, it fixes the sum of the top- and bottom mic but suddenly the bottom mic is not properly capturing the movement of the bottom skin. Tricky business.
That's why they do them holes in the side of the snare.
So sometimes you actually need to flip the polarity of the bottom snare due to other reasons than the good old "it's pointing towards the top mic".