In reality, it has nothing to do with the military and everything to do with being able to survive. The dome is actually part of a water collection system since fresh water was a continuing problem for those that lived out on Point Reyes. As explained on an information placard by the concrete dome:
Although surrounded by seawater, the Point never had adequate wells or springs to supply fresh water. The lightkeepers were forced to devise this elaborate system for catching and storing rainwater. They piped the cistern water to the residences and down to the fog signal for making steam.
The dome in front of you covers the cylindrical concrete cistern. The catchment area around the cistern extends far up the hillside and captures runoff from natural rock formations.
The information sign can easily be missed because those arriving tend to focus on the visitors center and the sign is around a slight bend on the way out.