Due to a problem in the Quartus® II software version 15.0 and earlier, the Quartus II software fitter allows an unsupported registered phase compensation FIFO setting for channels 1 and 2 of Arria® V device transceiver banks GXB_L0 and GXB_R0?
The restriction in the Arria V device handbook is correct. There is no support for registered phase compensation FIFO mode in channels 1 and 2 of GXB_L0 and GXB_R0.
You should not use the phase compensation FIFO in registered mode for the above channels.
This problem will be fixed in a future version of the Quartus II software.