I saw this scene rather differently:
Your sibling tells you that they dont want to be girl. You are not sure exactly what they are aiming to say exactly, so you respond carefully with further inquiring (not that you dont understand what does it mean not wanting to be a girl, but not undersanding exactly yet what your sibling want to say in the end)
So your sibling tels you that they dont want to be neither boy nor girl. Then you nod thats ok, you dont understand the feeling yourself, as you havent had that feeling, but game narrates that there were some children who did similar declaration in the past, so the fact of declaration is not new.
Then you reasure your sibling, bringing the fact that others sometimes feel just like them.
Then you feel proud of yourself that your sibling trusted you first with that, and proud for such young child to be confident with their emotions.
I dont see ““no problem” to “I don’t understand”, to “I’m so proud of you” in something like 10 minutes.” Your character is established what they know from the beggining. They do not see the problem with being non-binary, they dont completely understand the feeling, since they havent had it themselves, and they are proud of themsleves and the sibling for confidence.
You get a page of story that is an exposition how in this village/society being non-binary is perfectly fine with everyone.
You didnt get an option to choose the response for that, because that part is the established part of this game world, the same as many other things in game that are established and you dont get an option to choose.
Because that’s apparently significant part of their identity decided for that game. And why not? There is really only a little about our sibling and that fact ties to the exposition of the village and gender norms in game’s world, so the game focuses on that. And it’s not even like your sibling mentions it in every toher sentence they are non-binary.
So you prefer when a game only mentions briefly LGBTQ characteristic and then let you forget that those people exist? 
You dont like when it’s “forced” upon you that you are ok with non-binary people and making no big deal of it? You can’t just believe that your character could just treat it like a normal thing, and you need whole long detailed explanation why would you be ok with that?
How does it hurt the story, if your character is “forced” to just not be a bigot?