Why SATA ALIGN primitive is shifted or swapped on 7-Series GTXE2 transceiver RXDATA output?
I thought again about your inversion problem. The problem is that you or your PCB or your device swapped the RX+ and RX- wires for the transceiver input.

Your GTXE2 is configured to a 20-bit bus and no 8B/10B encoding, so the direct inversion of each bit seen in your measurement is caused by the wrong polarity at the input pins. You can enable polarity inversion (RXPOLARITY) for RX in the transceiver. The option is used to swap the pins, because PCB designers might swap the wires to reduce hops and vias.

You should also look into your boards schematic if there is a hint for swapped wires.