After some further thought on the matter, I am not sure whether or not calibration with the Trackimo mounted is the answer. Any magnetic interference from the Trackimo's electronics will indeed be constant with respect to the AC, but it will not be constant with respect to magnetic north.
Oversimplifying, and ignoring that there are two compasses on the aircraft, assume for example that the AC is pointed at due magnetic north and the Trackimo is creating even a weak magnetic field that "attracts" the AC and the Trackimo is mounted at the rear of the aircraft. If the AC is pointed due north, the "pull" of the Trackimo will be toward the south and therefore on the north-south magnetic line and will not affect the AC's reading of magnetic north. The same goes for the situation where the AC is pointed due south. However, when the aircraft is pointed some other direction, there is going to be an east or west error. Assume in our situation that the AC is pointed east but the Trackimo is "pulling" it west, the AC compasses will read that the AC is pointed east of north. Or, if pointed west, the AC compass will read it as west of magnetic north..
Never understood why before, but when I used to fly single engine airplanes, the compass correction card always mounted in them, would give different magnetic corrections for different compass readings. North might be one degree of correction while east might be 3 degrees correction, south 1 degree and west 2 degrees.
I am guessing that the magnetic field form the Trackimo is fairly weak, though I would also guess that the compasses in the Mavic are fairly sensitive. On the last set of test flights where I was getting no errors without the Trackimo mounted but compass errors with it mounted, according to Airdata, those compass errors were low risk. So maybe it is still safe to calibrate without the Trackimo on the AC and maybe any compass error induced is small enough not to cause serious issues. I have heard that if the IMU heading and the compass heading disagree there is likely to be a fly-away, but maybe in my case, the disagreement is small enough not to matter much. More testing is in order. Or at least so I hope.
I would also note that I experienced problems calibrating the compass with the Trackimo mounted. It simply would not calibrate at times,
I hope someone more knowledgeable than I see this thread and comments.