The vehicle will only accept RC messages from the GCS, you should be able to run both mavros and QGC with the same ID, at least that what I tested a couple of years ago working on the BlueROV2 playground for ROS.
You can check it here: GitHub - patrickelectric/bluerov_ros_playground: Scripts to help BlueRov integration with ROS
I would also recommend to create a .lunch file to organize your startup setup.