I’m tackling this for the first time in detail as I write my first ChoiceScript game, and it’s already proving to be an interesting and challenging prospect, especially as I chose from the start to depict a somewhat gendered world.
I think you summed up quite well my favoured approach already (“write them with humanity and thoughtfulness, and don’t be weird about it”), a.k.a. what I like to call the GRRM ethos, and this goes for all colours and classes of people. On the face of it, it seems very simple–like a starting point for beginners–but I think it’s really at the core of good character writing and is the foundation for everything that comes after.
What it means in practice (at least for me), is really sitting down and wrestling with what makes each character who they are and the interplay between those things: their flaws, their fancies, their foibles, and their contradictions. This includes traits like transness, gender, race, body shape, and more, especially in any world that put emphasis or draws attention to one or more of those traits. But this does not mean that any character should ever be defined by any of those traits–this is bad character writing, whether the overbearing trope in question is that they are gay or that they are heroically selfless, because no one in the history of humanity has ever been uncomplicated.
The article you linked touches on this a little too: I think for minorities of any kind, identity sanitisation often leads to a feeling of disconnect, or disingenuity, because writers aren’t truly reckoning with what those traits mean for the character themselves and every other person who interacts with them. Coming out stories and gender identity reckoning stories are great, but they cannot afford to exist in a vacuum, even when they are the entire focus of a piece of work, because we as people do not exist like this, and neither should any believable fictional character, whether fantastical, historical, or mundane. I think the kind of “flat” writing is a good start, but I think it’s where I see a lot of well-intentioned writers stumble the most. It can often be interpreted as “representation for representation’s sake” or “cookie-cutter representation”, and readers, even very progressive ones, might get the impression that the writer is trying to fill a quota. Sometimes they are, and that’s actually OK too! Some writers have to fight their internal biases and “add” representation where they wouldn’t have usually thought to include it–this is, definitionally, “meeting a quota” for representation, even if said quota is an arbitrary number in the writer’s head–but the sticking point is when the subsequent work is not done to fit that character into the world and the wider cast and actually address the now-changed context of their existence.
This isn’t to say that every piece of work has to have a deep, philosophical dissection of gender identity and societal norms on every fifth page. Many pieces of media recently have opted for the “everything is accepted” approach (see also: “I’m gay, but world is ending, so I don’t really have time to talk about it.”), which is perfectly valid–in fact, it’s what a lot of people seek out now, because it’s comfortable. The thing is, this approach works because, in a way, it still does exactly what I’m talking about above: examines the character in the context of the world, and presents them accordingly. It defines character traits, decides which ones are the most impactful and important to the character, then dives into them. In a world where being trans is as mere a fact as is the colour of your hair, why would the story make a big deal out of it? This is simply the other side of the same coin, in my view, and allows players and readers to see themselves or otherwise roleplay a wide variety of people and identities without the discomfort of interacting with a potentially triggering or too-realistic-for-the-current-era-holy-fuck-what-is-happening-to-the-world setting. But again, even in this wonderful world, no human is uncomplicated, no minority is perfect, and no two stories of self-discovery are the same; if you’re not careful with this approach, you’ll fall back down the “cookie-cutter” rabbit hole, where characters exist to be representatives and not people, which should always be your number one goal.
I’ve waffled a lot about minorities in general, but to bring it back to the specifics of trans characters for those reading… I really like the practical advice Harris has given in their blog–they make great “next-step” questions for people to think about when writing trans characters specifically. They’re great questions you can ask yourself about your cast and setting to start getting in the right headspace for all the stuff I posted above. To add my own, I would consider:
- How do non-trans characters in your story interact with the trans characters (including, potentially, the PC)? Indifference? Excitement? Fear? And more importantly, why? What drives those feelings–are they societal, or personal? Another tip: if all of your characters react the exact same way to a trans PC or NPC coming out, you might need to think about it more. Even in a trans-inclusive utopia, no two people have the exact same idea about transness, whether cis or not.
- For each trans character, how important is their transness to their self-identity? And again: why? And again again: what is this informed by? For many of the aforementioned “utopian” settings, most trans characters will not often think about it, but that doesn’t mean it means nothing to them! Being trans can be hard even in such a world, especially if medical and/or magical options for transition are limited, painful, cost money, or are in any other way prohibitive. Some characters might regard their tribulations as meagre when compared to other difficulties in their life; others might find them gruelling and look back on their transition with discomfort; others still might wear it as a badge of pride–a symbol of a challenge they overcame.
- This one’s not a question, but a little exercise, so to speak. Spend some time reading trans subreddits or forums. I know it sounds silly, but just listen to how people talk about themselves. Pay attention to the things that bring them joy. Not the big things, like gender euphoria when putting on the right clothes, or feeling seen as oneself for the first time, but the little things, such as, “Oh, I think HRT made me go down a shoe size, so now I actually save a bit of money because I don’t have to buy women’s shoes in larger-than-usual, harder-to-find sizes, and so now I have more disposal income and saved up for a gift for my boyfriend, which he loved, and that brought me so much joy.” These things might seem silly, but they’re authentic, and that’s at the heart of what makes good stories. When you’re always writing about the obvious things, those things don’t seem meaningful, because it can seem like you’ve just gone down a laundry list of “trans joy moments", and not really thought about or understood any of them.
This last point leads neatly on to a conclusion of sorts, as well. Ultimately, I believe that being a good writer is about being a good human–it’s about listening to people and trying your hardest to understand them, whether you share nothing or everything in common with them, whether you hate everything they stand for (a good villain is complicated, too!) or would die to protect them. It’s also why Terry Pratchett is my favourite author. He understood people better than anyone, and it shines through in all of his work. (Also a trans ally, by the way.) Stop, listen, read, and think. Sounds trite, I know, but it works. 
