As see on shematic few iMX6 boards, RGMII PHY put to MAC 125MHz to ENET_REF_CLK/ENET_TX_CLKENET_TX_CLK pin.
What it for?
I can't see any describe of this in manuals and RGMII not require this signal.
GPIO_16 is for RMII reference clock;
ENET_REF_CLK is for RGMII reference clock.