Hi Eliot,
I was able to figure out a solution after reading your thoughts. In my C++ code, I found that if I sent the mavlink message to control the motors with the sys_id of the Jetson nano, it was sending as ID 245. As you know, the ID of the GCS is 255. There is a line of code in Ardusub that says to ignore any incoming manual_control messages if the ID is not 255. So from my C++ code, the ROV was quietly denying my messages. They would show up in QGC, but no change in the RC output would happen.
I am still unsure what the issue is for my Python script, but my goal is to use C++, so I am not going to pursue that further.