Wow thats awful and totally not something people do with hetero pairings as well. Lucia and Aymeric have never been shipped by anyone after all.
The political issue is over things like discrimination and legal recognition. Not the very existence of LGBT people, unless you're completely out of it of course.
Why wouldn't it go through their heads? There's for sure LGBT people working at Square, hell they were at 41st Sydney Gay and Lesbian Mardi Gras https://na.finalfantasyxiv.com/blog/002680.html
And you're entitled to your opinion, I just disagree and will make an argument for why. The fact that so many people are desperate to shut down is what bothers me, especially since there isn't even a single out character in the game.