I'm not particularly bothered but mainly because the sexual tastes and orientations of the NPCs around me don't come up regularly, like if Alphinaud was dating a boy or something then yeah, sure, introduce his boyfriend during a cutscene or something stupid, but there's way more going on in the story beyond who or what Alphinaud is attracted to... Like, don't get me wrong, but with all the fighting against world ending threats and delving into the mysteries of Primals and Ascians there's not much time for characters to be really blatant or vocal about their orientations, I think the closest is maybe Alisaie and Tesleen where they could've hinted the two were in love or something without it being really shoehorned in.
As for the random city NPCs and basically filler content it's just not that important really, do you really need the baker in some shithole village hooking up with the florist of the same gender to get some representation? I mean, like, the world outside of actual characters is blatantly boring and pointless, I fly through these little villages without a care in the world and I don't really feel like anyone out there SHOULD be invested in them, they're nameless faces recycled with different clothing pretending they have some vague kind of life beyond just being decorations.
Would I have liked to see some gay characters in the roster of ACTUAL characters? Sure, but SE did give us the most important representation LGBT players can have, namely same sex marriage.
In this game you, the main character, can be 100% gay and you can be 100% with anyone else of your mutual choice, and it's something that has an actual vague impact on the game (the teleportation ring namely) and that to me is way better than NPCs awkwardly bringing up their sexuality or gender identity in what is a story revolving around the fate of the multiverse. Again, don't get me wrong here, it'd be nice to have a side story or a little quest chain about helping one of the NPCs out with a date as just a little fun thing to do, but I'd really rather not have gender/sexual choices being kind of awkwardly inserted where it really doesn't belong just for some vague 'representation'...
You can be yourself in this game, no one judges you for it, isn't that WAY more representation than 'oh those gay village dudes with no name'.