If you look at WW2 photos of embarked land units being carried on amphibious craft like LST's, you will see that the land AA guns (50 cal quad and 37/40mm mostly) are indeed deployed on the decks of the LST's, ready for use in their primary role even though embarked. This was also true of German AA guns embarked on their Siebel ferries in the Mediterranean, e.g. during the evacuation of Sicily, where AA guns up to 88mm were set up and successfully used to defend against air attacks. So there is historical and technical precedent for this.