It's possible, probably even more than likely, that just like EGS and Sony, Nintendo has paid for the exclusive window.
Take World of Final Fantasy for example, no where is Sony credited for development or trademarks/whatever, yet they managed to secure a year's exclusivity. And I mean, it's probably not because SE was feeling generous you know?
While I very much agree with your theory, i think citing Square Enix is a bad example.
They're so all over the place with their game launches in regards to platforms, i don't believe anyone is actually paying them for anything, they're just disorganized.
Final Fantasy VII rereleased on PC a year before PS4
FFIX was supposed to release on iOS and Steam simultaniously first and consoles later which then turned into iOS first, then steam, and then consoles.
Then you have Final Fantasy Tactics which to this very day is stuck with nothing more than a mobile rerelease.
Then you have the Last Remnanet Remastered which is a PS4 exclusive despite already having had XBOX and PC Releases for the original
And so many more situations like these.