Hi @rdehart,
Interesting, I wasn’t even aware that PX4 has (some) underwater vehicle support. Out of interest, why have you chosen PX4 over ArduSub? 
It’s been a while since I looked around in our old Companion Software codebase - do you have a particular reason not to use BlueOS? Granted it also doesn’t currently have Pixhawk 6X detection, but that’s something we could add if you can provide us with the relevant information, or you could submit a pull request with the relevant changes
I believe query-udevadm.py is only used for showing the Detected Devices on the web interface. You can add the information there if you want, but it won’t enable the MAVLink connection.
By default the MAVLink connection is configured to /dev/autopilot. If you’re ok with it being manual, you should be able to just put your own device path there if you want - the MAVProxy settings are accessible via the web interface.
If you’d prefer to have it automatically detected then you can add a line to the udev rules, and then copy the file over (like is done in setup.sh).