The polarity can be swapped on the USB 3.0 differential pairs. Polarity detection is done automatically by the USB 3.0 PHY during link training, as defined in the USB3.0 specification section 6.4.2, and does not require any additional changes to device firmware. Given the different USB connectors pinouts, the polarity inversion mechanism can be used to ensure that USB traces do not cross each other.
The same can be found in page 16 of the Application Note AN70707. The link to the same can be found below: