If you want to oversimplify things, sure. Let's not act like this guy wasn't saying that the game paints an image that girls can't be heros and that's why he's editing it, and that's what I have a problem with.
But it does because the definitive character of the series is Zelda and she is specifically a girl. This isn't Orcarina of Time where she's secretly being a hero, she stays in her tower like Repunzel and then gets kidnapped by Ganon.
Hell, who are the female characters in Wind Waker again? Granny who makes you soup? Zelda who gets kidnapped? The girl who kidnapped who started the whole story (because she was pretending to be you, a boy? really, i don't remember that much about it)?
Link is such an androgynous character that changing the pronouns relating to them is about as insignificant and shocking as how it's done in the book Orlando. Well, Orlando is probably a little more significant in its meaning for why but still, it doesn't change the character.
The character's heroic qualities juxtaposed against the other female characters shows differentiation among people or just character weakness to plot advancement. When Link is under the pronouns of 'he', it's able to become a gendered game on women being in the kitchen or under the protection of men, and I wouldn't even make those arguments. Someone could, but...
holy fuck someone changed the pronouns, miyamoto-san, forgive the sins of this one gamer and do not scorn us all