Solution:
The only requirement is to power-up the channel 1 of the used quad even if this channel is unused.
The rest of the unused channel/s can be left floating or not connected.
Refer to Section 13.5 of the CertusPro-NX SerDes/PCS User Guide (FPGA-TN-02245)
Note section:
Channel 1 of the used quad must be powered even though channel 1 is unused in this quad.