Hi,
why? It's a phase offset of 180°. In the most cases receiver and transceiver ref clk is not from the same crystal so you has still an offset when you start and and you always have a slight drift.
Receiver will make CLK recovery to align data. It is important that the accuracy of the reference CLK is within the required range.
In case data path of the lanes are swapped, you can easy invert (some protocols does it automatically). In case of JED IP core, enable debug pins and invert manually if necessary.
br
John