That's for you to decide. In my opinion, Naughty Dog is not structured that way, what makes their studio great is the collection of some of the most talented people across various fields that come together to make something special.
EVERY gaming studio and movie studio works that way. Every movie has a screenwriter, cinematographer, editor, camera men, actors, stunt cordinators, 3-4 assistant directors who lead second units, CG artists who mocap and animate everything and composers who make everything so memorable decades later. Where would spielberg be without John Williams? Or Nolan without Hans Zimmer?
There are like two directors who know how to do every job on the set. David Fincher and Stanely Kubrick. One of them is dead and the other still lets everyone else do their job because even he knows he cant do everything by himself.
You brought up Kojima. Look up the credits on who actually directed the cutscenes in the early MGS games. Look up the story credits. Game design credits. Kojima was not a one man show he is today. I am not the biggest MGS fanboy anymore but I remember the lead writer leaving after MGS3 and the result was a very bloated and very odd MGS4 and MGS5, and everyone pointing to his departure as the key moment when the series storytelling went to shit.
So yeah, even Kojima needed help. Should we find that writer and have him get credited whenever they manage to release the MGS movie? Of course not. The idea was Kojima's. He created the franchise. Others helped him but he was there on day one. Just like Neil and Bruce.