I wasn't around for the initial discussion about terminology and slurs, and had originally intended to let it lie because of that, but it wasn't sitting right with me, so here's my two bits.
Minor thing that irked me: people disagree about the shape of the Earth. That doesn't mean that the planet's shape isn't objective fact.
Anyways, on to the main point: while I can see the argument for reclaiming terms, I personally come down on the side of expanding the lexicon. While some people may like and self-identify as "tranny", "shemale", or "trap", some people are going to be hurt by them. With the terms originating and still being commonly used by transphobic people as slurs, it's inevitable that people will be hurt by those words because of what they represent, and unfair of anyone to blame them for it. Humans live in the stories they tell themselves about the world and their place in it. The stories conjured by those terms are frequently derogatory, painful, and humiliating, even if that wasn't the author's intent.
Writers have some responsibility for the effects of their words. Therefore, I'd urge all the writers to give the matter some serious consideration before using words that can and in all likelihood will hurt some of the most marginalized and vulnerable people out there. I'm not calling anybody out specifically with this. I have no way of knowing what thought process you went through before using the words, and I haven't paid enough attention to be able to fairly and fully judge them in the context of the game. I just want to ask that writers in the future be careful when using any fraught words or situations if they weren't already doing so. The world can be a cruel place, and I believe TiTS is better as a place for fun rather than pain (unless you're into that).