That's just gibberish.
The game differentiates between theaters (no leader assigned), army groups and armies, which consist of divisions. Corps play no role at all. Nor is there such a thing as "a corps of armies". An army consists of corps, not the other way round.
There was not a single point in time during the war where the Marines were actually operating on a scale that is similar to an army. And only once was a general from the Marine Corps assigned to lead an army. This was a temporary assignment after the former general had died, and it ended when General Stillwell arrived to take over command of the 10th army.
Since the game doesn't have any command structure below an army, and the Marine Corps never had an army of its own during the war, it therefore is perfectly logical to keep naval infantry under a general command. Especially when you consider that the armies in the game can actually be far larger than an army really was during the war.
All that is beside the point though, because you are conflating stuff that isn't connected. The game doesn't have "The Army", "The Airforce" and "The Navy", instead it has land formations, air formations and sea formations, all kept apart and used in combat interactions that are barely connected to each other. Sea formations represent all combat made by ships, they do not include men who invade beaches, because men aren't ships, and ships don't land on beaches, at least not on purpose. The only case that can be made, is that some leaders, like Roy Geiger, should be available as leader in the land-warfare branch, maybe with the invader skill that enhances naval invasions. Because that's exactly what these skills exist for, and that's exactly the place Marines fight on: land, not sea. They might temporarily engage in combat while still being in water - that's the point of a naval invasion after all - but they aren't meant to fight things on the sea, they engage enemies who are on land, and they do try to take that land, in prolonged operations of land combat.