I have a Navio2 board and the external GPS/Compass
The board is mounted pointing to the ground (Pitch-90) as it’s a SingleCopter and the external GPS/Compass is the right way up but pointing to the rear (Yaw 180)
For some reason, the heading is off by about 30 degrees.
I was hoping that there would be a slider 0-360 where you can offset.
I have found COMPASS_AUTO_ROT (2) to work well in determining orientation during calibration and setting it right. But to answer your question a custom orientation is possible if you want to run the -dev version of firmware:
From the Install Firmware page of Mission Planner Cntrl>Q will load the Master (dev) versions. If it doesn’t left click in the main window and try again.
But heed Andy’s warning about the custom compass feature having bugs!!