The MX6QDL_PAD_GPIO_16__ENET_REF_CLK refers to the ENET_REF_CLK function trough the GPIO16 pin. This function varies between the different Ethernet modes. In the case of the SABRE board where RGMII is used, this function is used as an input for the 125 MHz clock.
The PAD control for this pin is located on Register IOMUXC_SW_PAD_CTL_PAD_GPIO16. Details on this register can be found on section 36.4.386 of the i.MX6D/Q Reference Manual.
As for the way the device tree pin control works, you may find more details on the following document:
Documentation/devicetree/bindings/pinctrl/fsl,imx-pinctrl.txt