You're perfectly right that if RJ wrote Aran'gar to represent gender dysphoria or transgenderism, there are all sorts of issues that would make this an extremely toxic representation. But there's no evidence this was the case, nor does it have to be.

The only issue that matters is that the character refers to herself as female, as do all her colleagues whose PoVs we have thinking of her. And from those PoVs, we see absolutely nothing indicating that they're doing so in a derogatory fashion, as could be expected from the Forsaken.

The issue is that you took the trouble to convert "she", as used by the books and the author, into "it", which is dehumanizing to any living person whatever the context.

You need have no sympathy for Aran'gar, or think of her as some kind of representation of transgender people, to see the transphobia in calling her "it". The causes and manner of her transition are literally unrealistic, as is her swift adjustment. But that is what the books show happen. Case closed.

The issue would be similarly bad if you used racially charged or sexist language about the Forsaken. Sure, they're evil and no one's idea of representation of racial minorities or women. But if you use such language about them, you'd reveal your disdain and disregard for people different from yourself.

It is a strawman to argue that abusive language directed at terrible people doesn't matter. Your usage wouldn't be any worse, and would be just as angering, if you'd used it for some hypothetical hero who was a male soul born into a female body due to something the Creator does. That valence, of whether the person is good or not, simply doesn't matter in this debate.