If you happen to run three clusters of mag sensors (X,Y,Z on each wing tip and another group of three on a tail boom) then you are measuring a differential field against three points for each axis and sensing the induced ground change from a diurnally fluctuating field .. also getting different results depending on whether you are traveling North to South, East to West, or at some other angle.

Despite all that, maps are still produced of the leveled and normalized ground field (see geomagnetic maps).

Using the geomagnetic as an assist / backup to navigation reduces to something similar to the use of a DTM as an assist - not much use in flat areas, useful in areas with distinct features, easily confused if one valley looks much like another.

The daily flux is an issue, of course, but your software, hypothetically, would be looking at the preserved shape of waves on the ocean despite the fact that the tide is rising and falling all around.