Says who? As a subsidary of the broader Nintendo company, NoA has ownership over the Zelda franchise, and is therefore within their rights to do whatever they want with a given part of said franchise; this includes making decisions in localizing a given game that change certain plot elements of said game.
Is DigificWriter correct when he says that NoA is able to alter the plots however they want via localization? I doubt it, as localization is generally meant to convey a plot rather than altering it, and altering the plots could create different timelines in every region of the world and thus ruin Nintendo's efforts to connect the games.