Hello! There are several answers to your question, and none of them are great!
The first answer is “why not?” At the beginning of writing, I couldn’t think of a good reason why the Taiga dwellers had to be beholden to human gender constructs. I also did it because there are many scenes where the dialogue bounces between internal-Charlie-animal-speak and external-Charlie-human-speak, and I figured using they/them for the animals would be a good way to broadly gesture to who is speaking.
Finally, I was very new to Twine & Harlowe when I started, and at the time, I couldn’t come up with an efficient way to switch pronouns in dialogue based on your choice of squad. Using they/them kept everything consistent as the squad changed from player to player.
In retrospect, these aren’t great reasons to do it, and I doubt I would do it again. It feels weird to me now to use they/them pronouns on a structural basis without explicitly characterising the animals as nonbinary. But maybe I’m being too critical? I dunno.
Does that answer your question?