Received data alignment in the Custom PHY must be controlled via the Avalon-MM PHY Management Interface.

For details, see "Altera Transceiver PHY IP Core User Guide" p9-24 to p9-28, Table 9-18: Avalon-MM PHY Management Interface, and Table 9-23: Custom PCS in the URL link below. Please refer to

Altera Transceiver PHY IP Core User Guide URL:
 https://www.altera.com/en_US/pdfs/literature/ug/xcvr_user_guide.pdf