Hi enc0der,
To control GPIO in JP6.x manually, you have to apply the following patch.
40hdr - SPI1 gpio padctl register bit[10] effect by gpiod tools in JP6 - #20 by KevinFFF
We found gpiod command would set bit10 causing it configured as SFIO instead of GPIO.
Yes, GPIO can work as expected if you’ve configured it correctly.
Please just note that sysfs method to control GPIO has deprecated in JP6.x. We would suggest using gpiod instead.
Please note that pinmux/gpio dtsi are loaded in early boot(MB1) rather than kernel. It is not relating to the one your specified in FDT/OVERLAY entry in extlinux.conf.
As a result, you have to reflash the board to apply the change.
If you do not want to reflash the board, there’s a tegra-pinctrl driver can help to reconfigure the pinmux in kernel. (it is also how jetson-io works). You can try to add related configuration in kernel device tree for your use case.