Yeah, I fully understand that it's been put in there to allow the player to have full choice. After all, it'd be a shame if you're a guy and you like <Guy B> in the game, but only <Guy A> is bi/gay.
And I also understand what you're saying. True enough, taking Stardew Valley as the example again, for the first playthrough only the same-sex character you romance will be gay. This would be fine if my knowledge of the game is confined to this one playthrough only.
But my knowledge typically isn't confined to this one playthrough. I mean, in a next playthrough, or in someone else's playthrough, said character is suddenly straight. This breaks immersion for me (which I argue is important for Stardew Valley) since there is nothing in the game that prompted a sexuality change, unless we believe the player character is that charming that he/she can turn gay anybody previously straight.
It's a tricky topic with no winners. Because you definitely do want to give freedom of choice to players. It's important. But you also don't want to break immersion. Luckily for others, this freedom of choice isn't immersion-breaking for most, so ConcernedApe was right in choosing this freedom for the players over the immersion for just a select few. (And it's not like I hated the game because of it, so...)
But I am glad that there are also a few developers out there who do think "Well, hey, not all characters are bi. That's just how it is."
That said, I don't know too much about Fire Emblem yet. I've just started playing the GBA game not too long ago, in preparation for the Switch game. I'm trying to work my way through all important FE games
EDIT: Even though my comment is already really long, let me clarify a few more things.
With the same reasoning, I also think it's immersion-breaking if every opposite-sex character is romancable. I don't know how Fire Emblem does this, but if every character there is a potential romantic candidate, then I'd find that equally weird.
I mostly come from Visual Novels, where there is typically an arrangement of 5 girls to date for the main character. Also there I would find it weird if those 5 girls were the entire cast, meaning that 100% of the female characters is into the main character. Yikes. Talk about unrealistic.
Sadly, a lot of VNs are like that, but that doesn't mean I think it ruins the VN. As long as the story and art direction is good, I'm into it. And I'm sure it's the same for Fire Emblem. Even if there are aspects that break the immersion, as long as the story and gameplay and such are top-notch, it won't ruin the product for me