Sunless Skies has the Incautious Driver who's enby and the Fortunate Navigator who's a trans guy. For both it doesn't feel tacked on but doesn't define them either, which is cool

For those into (not porny) dating sims, Date Everything very probably has both. (I have only discovered a very small part of the characters for now, so I have not verified it.) Warning though: every NPC in this game is an anthropomorphised domestic thing (objects, appliances, dust, etc).

Stardew Valley's expansion mod Ridgeside Village instroduces a ftm character. I will not say his name for spoiler reasons, but he's quite a touching character IMHO. (Well, although unoffical, he is a befriendable and romanceable Stardew Valley character after all.)

Not 100% sure on the validity but I read somewhere that Party Girl (one of the villager NPCs you can build a house for) from Terraria is trans.

• Kris from Deltarune and Frisk from Undertale are both non-binary, though they never tell us their agabs (fair)
• Kirby, while using he/him pronouns in the english speaking world has always been genderless and even hangs out with the girls in a nintendo promotional panel where a bunch of nintendo's female characters bake together. He is also seen in the equivilent nintendo boys content
• Birdo from doki doki panic and the Mario franchise is mtf
• Vivian from Paper Mario the 1000 year door is mtf
• The player character in hollowknight is some sort of eldrich thing pretending to be a child, so falls into the genderless monster trope
• Cyberpunk famously allows you to create a custom character who is male, female or some combination of the two
• Saint's Row 2 has a gender slider where all the way to the left makes your boobs bigger and all the way to the right makes your dick bigger. I can only assume right in the middle to mean non binary.
• Every saints row game between SR2 and SR2022 has plastic surgery clinics where you can change your gender pretty much at will as long as you have the money. SR2022 replaces with a pause menu item which is better for convenience but less fun from a worldbuilding standpoint.