Re: Naruto and Hinata confirmed as "Secret Lovers" in Shippuden Ninja Storm 3
All the developers got in relation to the original series were rights permission from the developers. They could put in whatever the hell they want in their games and all they would get in return is "Sweet! Money!"
In short, while they don't "put in whatever the hell they want" and instead bake fan cookies, you shouldn't take what's created in a video game as canon to manga lore; you're gonna have a bad time.