Ok thank you for confirming that the GPIO ALT should be possible.
Do you know of any testing that has been done to confirm this configuration? I see there have been software releases of toradex image that have had bugs that prevent control of certain GPIOs but not others (see discussion here: Some GPIO pins work as expectation, but some pins don't - #8 by tanchunhau).
We have attempted explicitly configuring the Pin control register per the muxing instructions. The GPIO remains accessible in gpioinfo as before, and is even shown as an output when our code is activating it, yet we still have no voltage change when connecting a logic level shifter (TXB0108) to LED+2k Resistor (low current LED). This same hardware test has been used to confirm the majority of our other GPIOs, these are the only 2 GPIOs that do not work.