Hi Rob,
Nice rig! Great to see the little GR under a drone

Your right, there's no way to know where the subject is. i'm not used to working with a drone ;-)
Underexposing seems the best solution, but only works if there is not to much white/light to be seen. Otherwise, the photos will be to dark. Also, if the ships are big enough, the lightmeter should have less trouble. Only when the ships are small and there is a lot of see/ocean in the scene, it's not an average scene for the camera.
So, lack of dynamic range could be the problem, if it is not recoverable in RAW. Bracketing would be the best solution, if this is possible with timelapse. But it slows down the camera.
But i am also wondering. Could it have something to do with the camera being upside down? It evaluates the scene in intelligent lightmode. but your sky is at the bottom

. Maby interesting to test this?
Regards,
Kees