Question: Can you swap the polarity on USB 3.0 Differential pairs?
Yes. Polarity detection is done automatically by the USB 3.0 PHY during link training, as defined in the USB 3.0 specification, section 6.4.2. Doing so does not require changes to the device firmware. Given the different USB connector pin-outs, you can use the polarity inversion mechanism to ensure that USB traces do not cross each other.