So...
1) They were designed this way.
2) If you want try to establish a certain absolute polarity, and you think you hear a difference, just swap the wires at the cabinet speaker terminals or at the amplifier. It won't harm anything, but I suggest you do both speakers if interested (although it's educational to do just one as a test, to hear what an out of phase speaker pair sounds like).
3) If you only swap the polarity of the woofer and change nothing else, you -will- affect the way the woofer and mid interact in the crossover region...
still won't damage anything, but it may sound different and have a different frequency response than stock. Benefit? Try it and and see. They're your speakers