The HTL Hatshepsut's main dock is at the bottom of a round structure on the ventral surface of the destroyer. The dockpoint itself seems to be at the bottom of a short tunnel or indentation in this structure. The result is that a small ship which docks there will actually sink into the ship's geometry, and disappear from sight. This breaks a mission I was just testing in which an Isis transport docks at this point, and then effectively is invulnerable since it is inside the destroyer's hull. here it is sinking in, eventually it will not be visible:
IsisSunk by
NelsonAndBronte, on Flickr