Cyclone V: PCIe x4 + XAUI.

Basically, Native Phy is just a transceiver/Physical layer used in XAUI protocol.

In order to fully compliance the XAUI protocol, you need to write a a soft logic such as deskew fifo to compensate the lane skews, rate matcher to compensate the ppm difference and other blocks that required by XAUI protocol.