Hi Skewmix,
Thanks for taking effort in posting the issue along with necessary inputs.
Pinmux register values seem to be wrong. They should be as mentioned in Audio I2S on 40 Pin Connector - #54 by jonathanh. I would suggest to redo the pinmux changes as guided in link. Yes, Jetson-IO tool works for dev kit only.
No need to modify any amixer settings or other register rewrites. The default ones should work fine once the pinmux is set as desired.
Thanks