The reference designs target both Zynq boards and Zynq MP (Zynq Ultrascale+) boards. The designs for the two target devices differ slightly due to the fact that the Zynq devices have only 2x GEMs whereas the ZynqMP devices have 4x.
In the Zynq designs, the first three ports of the Ethernet FMC are connected to the AXI Ethernet Subsystem IP which are then connected to the system memory via AXI DMA IP. The fourth port of the Ethernet FMC is connected to the GMII-to-RGMII IP which connects to hard GEM0 of the Zynq PS via the FPGA fabric (EMIO). The Ethernet port of the Zynq development board (ie. the on-board Ethernet port) connects directly to the hard GEM1 of the Zynq PS via MIO.
In the ZynqMP designs, all ports of the Ethernet FMC are connected to the GMII-to-RGMII IP which connects to hard GEMs of the ZynqMP PS via the FPGA fabric (EMIO). The on-board Ethernet port is left unconnected and is thus unusable in these reference designs.