Square Enix is both a developer and a publisher. So, a lot (I want to say most, but I really have no clue) of their games, like Final Fantasy, they made entirely themselves. Then you have a game like The World Ends with You, which was developed by both Square Enix and Jupiter... and a game like Radiata Stories, which was developed by just tri-Ace. So, since the publisher is paying to make the game, they really get most of the power, but... I figure it works like an author and book publisher, if you know any more about how that works. To be honest, I'm not an expert on the subject myself, but
these articles seem to be very helpful regarding what you're asking.
3nodding