This is a LOT better than my list which I gave up making not even halfway through. Thank you, for making this!
You mentioned in the description that you are open to suggestions so here's my minor input.
- Cyberpunk 2077's description says that you can create a custom trans character, however, there's also a fully voice acted trans character called Claire, who gives you the racing side-quests that might be notable.
- Hogwarts Legacy also has a trans side character, the bartender called Sirona Ryan in Hogsmeade. It also lets you create your custom character as trans.
- It's not out yet but I've been paying attention to Goodbye Volcano High, which according to their FAQ has a non-binary main character called Fang. Source: https://goodbyevolcanohigh.com/faq/
- The Sims 4 and Baldur's Gate 3 both let you create trans custom characters.
I'm setting my list to private so as not to divert any attention from this definitive masterpiece.

@mesterjani Thank you very much for these!! I appreciate them a ton ♡
I actually was aware of the character in Hogwarts Legacy, but given JKR's history of transphobia and the fact that she considers monetary support of the HP series to be support of her bigoted views, I actually decided against including the game at all. I know she wasnt directly involved with the creation of the game, but I still felt giving the game any attention would still benefit her. Hope this makes sense, thank you again for your suggestions!

Hi, again! Thank you for including my previous suggestions, I hope you don't mind some more.
- The Comic Wheel Sisterhood has a character who is struggling with dysphoria and the main character helps her out. You help her choose her name from a set of choices, so I don't know what to call her canonically, but I'm pretty sure she's referred to as The Peppermancer.
- Starfield lets you choose any Body Type, Walk Animation, and even pronouns including they/them.
Spoiler?: There's also a female character called Hadrian who is originally a "clone" of a man. I'm not sure if she classifies, but I did see a bald white dude having an embarrassing meltdown over it on Twitter, so I figured it might be notable.

I promise I won't spam you with these. It's your list after all. I also understand and respect your reasoning about excluding Hogwarts Legacy. I hope I didn't come off as one of those people by suggesting it.

@mesterjani Hey there, no worries! I appreciate these a lot, so by all means feel free to spam me lol. And don't worry, I didn't think badly of you for suggesting Hogwarts Legacy, so you're perfectly fine :)
Thank you again, I'm sorry it took me so long to get back to you!!

Adding to Mama from Somnium Files, an exchange in the second game suggests she has had bottom surgery. In Exocolonist, some dialogue if you pursue the medical career implies Utopia is a trans woman, something the devs confirmed directly to me when I asked -> https://twitter.com/AKANEOWARII/status/1647246843699515392

7th Dragon 2020, at least in the English fan translation, features a sidequest from a "transfixing woman" to retreive her "blue pill bottle", which she says contains hormones that are very important to her. Additionally, an NPC in the sequel, 7th Dragon 2020-II, will greet the party with "Mr, Ms, Mx Murakumo!", implying that at least one member of the player-created party could be non-binary.

@lesbiankakyoin @LunaFlare thank you both! ♡♡

I have a couple of suggestions if that's okay, sorry if they're already present and I didn't see them. In Stray Gods: The Roleplaying Musical, the latest incarnation of Hermes is nonbinary. In Harmony: The Fall of Reverie, Nora is a trans woman and Yana, Chaos, and Truth are nonbinary.

@TabletopRPGFan It's always okay! Thank you so much ^__^ ♡!!

For a suggestion I didn't see on here, The Arcana allows you to be nonbinary, one of the romance options (Asra) is nonbinary and uses he/him pronouns, and several major side characters (Valdemar, Nazali, and Vulgora) are nonbinary with they/them pronouns. There is also a minor character, Scout, who mirrors whatever pronouns your character uses, which can include they/them.

I see you already have Heart of The House by them on here, and I have no idea how you'd feasibly list them because there are so many games, but if you're not aware having nonbinary/trans options and diverse characters aside from yours are the norm for any interactive fiction game published by Choice of Games or Hosted Games! Off the top of my head a few notable ones are:

- Creme de la Creme (protagonist can be nonbinary, all romance options can have their genders selectable or randomised which both include nonbinary)
- Fallen Hero: Rebirth, Fallen Hero: Retribution (protagonist can be nonbinary; one of the romance options (Dr. Mortum) is trans, whether a trans man or a trans woman or intersex will depend on what gender you selected them to be; a major side character, Hollow Ground, also does the same as Scout from The Arcana in that they mirror whatever pronouns your character uses)
- Keeper of the Sun and Moon, Keeper of the Day and Night (protagonist can be nonbinary)
- The Wayhaven Chronicles (protagonist can be nonbinary)
- Heroes of Myth (protagonist can be nonbinary; Min, one of the romance options and a major character, is nonbinary and uses they/them)
- Versus (protagonist can be nonbinary; Prince Everly, a romance option, is nonbinary with they/them pronouns; Breeze, another romance option, is either a trans man, trans woman, or intersex depending on the gender you select for them; Oli, another romance option, at first appears to be whatever gender you selected but turns out to be the false identity for a character named Dhanthik, who is nonbinary and uses zie/zir pronouns).

@HaloBlues thank you so much!!