That’s by design – Plex currently prioritizes the configuration that an item should be displayed. There’s a feature suggestion to prioritize the configuration that an item should be hidden in the default library.
Right now the only way to achieve what you’re aiming for is to use a smart collection. Smart collections don’t impact the visibility of their items. This way you can e.g. group a smart collection Marvel Cinematic Universe (filter criteria: studio = Marvel Studios) which will contain all the different franchises (e.g. Iron Man 1-3, Thor 1-3, The First Avenger 1-3…) as well as their stand-alone movies (e.g. Black Panther, Doctor Strange, Captain Marvel…) where the franchise collections will hide their items while the individual movies will still be visible in the library.
