Looks like the watertight compartments and damage control scheme worked, since the ship is still on top of the water and apparently still on an even keel.
You're right about the Phalanx engagement envelope - the Phalanx is mounted on the bow and a sea skimmer from a quartering angle would be occluded from the Phalanx system by the superstructure.
Maybe our naval architects will rethink their removal of Phalanx systems in favor of RAM launchers....
The blast damage and blackening seems to me to indicate the missile came in at enough of an angle from the starboard side to allow the Phalanx to engage. I could easily be wrong and will have to wait for more data.