Why are the SSRX_N and SSRX_P pins swapped in the CYUSB3KIT-003? Is it possible to swap SSTX_N and SSTX_P? Is it correct to swap USB 2.0 differential pair (D+ and D-)?
The polarity can be swapped on USB 3.0 differential pairs. Polarity detection is done automatically by the USB 3.0 PHY during link training (called TSEQs), as defined in the USB 3.0 specification section 6.4.2. This does not require any additional change in device firmware. In the design of the PCB layout, SSRX_N and SSRX_P (or the TX pairs) may cross with each other. Inversion is recommended to avoid this crossing.
However, inversion is not allowed with USB 2.0 differential pair since inversion detection is not implemented in USB 2.0.