I used QGC for sensor calibration with pixhawk2, and found that the orientation was wrong. When I placed my pixhawk2 face up, the QGC showed it was downward. The orientation could be consistent with the calibration when I set autopilot orientation to “ROTATION_ROLL_180_YAW_270”.
px4 version: px4fmu-v2_lpe 1.6.5
The rotation that QGC shows comes from the firmware. Not sure if sensor orientation is taken into account prior to calibration or not.