Due to a problem in the Quartus® Prime Standard Edition Software version 21.1 and earlier, you might see the incorrect transceiver power rails in the pin-out file and the .pin file of the Arria® V device, 5AGXBB1D4F40, which shows both left/right side transceiver power (i.e., VCCL_GXBL & VCCL_GXBR) is connected.
The 5AGXBB1D4F40 device has only the left-side transceiver, you may ignore the right-side transceiver pins (VCCL_GXBR , VCCH_GXBR, etc.) and connect these pins to GND.