There's a difference between a game having homosexual themes and a game where same-sex relationships are an option.
With the former, the point of being gay is a main feature in terms of the game's themes. The LGBT stuff is there to tell... whatever it is the game is trying to say (I wouldn't know, since most of the games/stories I've seen all did the same story beats, so I expect nothing special for them). There's a bit of a gray area with this where some people will have same-sex relationships and not think them prominent enough to warrant tagging, treating it like a "them being gay doesn't matter" thing, but I wouldn't say one thing or the other without having any numbers...
With the latter, the entire point falls back into customization. By allowing the player character to romance NPCs of either gender, it allows for more customization options. If the player has the option to pick their gender at the start of the game (or doesn't specify), these relationship options exist regardless. Sure, it's not realistic for, like, 70% of the population of a town in some farming sim to be gay (and I'm not going to pull that whole "bUt rEaLiSm dOeSnT mAtTeR iN fAntAsY" shit or any similar argument since that's a stupid handwave), but there's not really a reason to restrict content that barely affects gameplay (usually marriage options are just cosmetics), so it's best to just not draw too much attention to any differentiations.