USB3.0 allows checking the polarity through hardware handshake and reverse the polarity if needed ( To make the life of PCB designers easy by making the routing of the USB3.0 lines easier). That is the reason behind the swap.
Coming to High-speed lines,
Avoid routing D+ and D– through vias; vias introduce impedance mismatch. Where vias are necessary(e.g., using mini-B connector) keep them small (25-mil pad, 10-mil hole) and keep the D+ and D– traces on the same layers.
Does the USB2.0 lines on FX allow to swap?
The document says "The polarity can be swapped on the USB 3.0 differential pairs." I'm confusing if the D+/D- pairs belongs to the USB3.0 differential pairs.
No, we can not swap USB2.0 lines. It is valid only for USB 3.0 differential data lines.