What do you mean about “custom version”?
Are you using the devkit or custom board for AGX Orin?
To enable SPI (no matter SPI1 or SPI2), you have to configure pinmux first, and disable the GPIO usage for those pins then loading the spi driver.
The overall steps could be found in the following thread, but that is for the Jetson Nano devkit.
Jetson Nano SPI Bus Not Working - #10 by KevinFFF