The craters' visual representation are 2D and not fully 3D because it would play havoc with other 3d elements (eg, a 3D crater next to a hangar might extend underneath it, etc), but according to previous feedback from developers and players you do suffer damage if you taxi over one just like it would be a 3D one.
So if a script can control the "rate of ground crews filling up craters", what you describe will be feasible.
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