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I still haven't played this VN, but I'm going to assume it's the following:
"They/them" can be used when you don't know the gender of the person you're talking about.
For example, if I were to tell my friend about your comment and my reply, I'd say "So, there was this user in itch.io with a question. [They] didn't know about the gender neutral use of "they", so I explained it to [them]".
So, in this case, [They] is singular, but genderless.