As shown in the Mallow schematic and the tables you provided, the mentioned GPIO pins on the Mallow X16 expansion header are connected only to the M.2 connector (X17). They are not routed to any Verdin pins, and no Device Tree modification can make them function as regular GPIOs.
The only way to utilize these pins as GPIO is by installing some kind of a GPIO expander to the X17 slot, controlled via either USB or PCIe.