If im thinking what you're meaning, then i think i have the answer.
I think we use Overall main antagonist for a big long running franchise like Emperor from Star Wars, Frieza from Dragon Ball Z and so on, or when there are to many threatening villains, we just say the one thats the most threat to the hero and has more or threatening goals.
Main antagonist is just the main threat towards the hero. Simple
Now im not an expert as i just joined the site but i hope im accurate