I'm sure this is a bug and not intended game behavior.
In this replay, at 30:30(ish), the grey commander is getting torpedoed. He gets on an air transport while torpedoes are incoming. The torpedoes pursue him out of the water, hit him while he's in the transport, dropping him back dow, killing him shortly after.
I'm sure torpedoes aren't supposed to be able to leave the water.
That's not what I saw in the replay.
It looked more like Gray's ACU was being picked up by a T2 trans, and then he gave the transport a different order, so it dropped the ACU back in the water. Where it died to torpedoes.