Hi ZXZhang,
It is not the expected operation to me.
gpio.dtsi has been inlcuded in pinmux.dtsi so it does not need to be specified in board config.
GPIOINT_CONFIG is used for gpio-interrupt configuration.
Do you modify any line relating to bpmp-dtb?
To control GPIO with Jetpack 6.x, please also apply the patch from the following thread.
40hdr - SPI1 gpio padctl register bit[10] effect by gpiod tools in JP6 - #20 by KevinFFF
Or you can use Jetpack 6.2.2(r36.5) which should include that patch.