The magnetics don't care about the polarity of the pairs, in fact the PHY doesn't care either (well, maybe some PHYs do, but that would be very unusual). Even if you use the 'right' polarity throughout your design, it may end up connected to another device that has the polarity swapped, so it really doesn't matter. PHYs are generally designed to tolerate this, so you're free to swap polarity within pairs in whatever way makes your layout easier. You can even swap TX and RX pairs if your PHY supports auto MDI-X, which most do these days, but check the datasheet to be sure. Usually it's enabled by default, if not you can use the PHY's management interface to configure it.
EDIT: just noticed your part number, the LAN9354 actually calls out automatic polarity correction along with auto MDI-X in the first page of the datasheet. That's unusual, most devices don't even mention polarity correction because it's just assumed, except maybe in calling out a bit in a status register that indicates the link polarity. I guess someone wanted to fill out the feature list a little to make it look better