I do not have such high offsets with my original Navio. I will try and run APMCopter with it and see how high the offsets are. (oh no, juggling my rover again…:-()
You can not simply connect the external compass to I2C. I had compass problems with my Navio (not +) before. Mikhail explained that the MPU9250 compass is handled as an external compass. You have to change some file and compile APM yourself.
Here is the thread: