You can fly over the same spot at four different times of day and get four different readings.

You also really want nine magnetometers, one for each X,Y,Z axis and repeated on each wingtip and tail boom.

If you're going to filter like a professional you need a base station to record the diurnal flux and subtract that in post, you also need to fly calibration clover leafs in a magnetically level wide area and develop a Kalman filter to subract heading generated flux.

There's also the active magnetism compensation caused by the aircraft and its components, such as engine accessories, engine masses, avionics, current generated on the fuselage and other factors. If you're running a small fleet of aircraft to cover a million line kilometers or are otherwise pooling results into a standard magnetic map collection each aircraft will need to have its signature influence removed.

If you're mapping entire countries over decades then, of course, everything needs to be levelled against the changing IGRF (Internatinal Geomagnetic Reference Field), or the other one (there's another standard global magnetic reference field).

Then there's the question of just how small an iron rich rock you could reasonably get a blip from.