So in your use-case, you use UART0 on the M2 key and see additional two bytes(two 0x00 0x00) in each transmission. Is this correct? And please share which Jetpack version you use.
I think the point with the “Disable Serial Console” is that you have to be absolutely certain that a second program (in this case a serial console) is not interacting.
Had this test not been loopback the stray NULL bytes could have been from one side having more stop bytes. If in loopback there are stray bytes due to stop bytes, then this would probably be due to something going wrong in the driver. If serial console is still active, then it isn’t truly loopback.