@WayneWWW solved this problem for us when he solved our other problem over at UEFI with RGMII is slow to boot. The key realization is that there are two device tree files to change.
To change pinmux and GPIO, change both
DTB_FILE = my-custom-board.dtb
TBCDTB_FILE = my-custom-board.dtb
This changes the pinmux and gpio for both the bootloader and the device tree.
Thank you @WayneWWW. Please consider this issue resolved.
-sam