Hi jack.yan,
Are you using the devkit or custom board for Orin NX?
Why you said that you want to use PY.03 but you are configuring PZ.06?
I would suggest configuring pinmux from pinmux spreadsheet instead of modifying pinmux dtsi directly.
Yes, please refer to the following topics for this use case.
Can’t enable PPS on Jetson AGX Xavier - Jetson & Embedded Systems / Jetson AGX Xavier - NVIDIA Developer Forums
AGX Xavier PPS fetch timeout R35.2.1(R32.7.1 works fine) - Jetson & Embedded Systems / Jetson AGX Xavier - NVIDIA Developer Forums
Pps_gpio interrupt not asserted - Jetson & Embedded Systems / Jetson Orin NX - NVIDIA Developer Forums
PPS input to GPIO on Jetpack 6.1 - Jetson & Embedded Systems / Jetson AGX Orin - NVIDIA Developer Forums