Here’s some more for you:
Not a Sidekick by C.B Lee has a trans character, though not a protagonist. That character IS a protagonist in tye second book of the series though.
There’s also the Tensorate series by Neon Yang. Each novella focuses on a different character, but a continuing story, and takes place in a world where all children use gender-neutral pronouns until they choose what gender they want to be as an adult.
The Empress of Salt and Fortune by Nigh Vo (as the other books in the series) has a non-binary and trans character
When the Moon was Ours by Anne-Marie McLemore has a trans character and a character who has roses that grow from her wrists.
Ninefox Gambit by Yoon Ha Lee has a protagonist that’s not exactly trans, but is female while also playing host to a male character, and you just kind of have to read it to get it. I will warn you that the worldbuilding, while fantastic, can be above a lot of heads and there’s not much gritty explanation. The author throws you in the deep end with terminology and the reader either goes with it or doesn’t.
The Cemetery Boys by Aiden Thomas - the protagonist is a trans male whose father refuses to admit it and won’t let him take part in the brujo ceremony. Hikinks ensue.
Also by Aiden Thomas, The Sunbearer Trials. I haven’t read this one yet, but I really want to.
Melissa (formerly titled George) by Alex Gino - MC is a middle-school transfemale who is not out, but her school is putting on Charlotte’s Web and she wants to play Charlotte, even though everyone thinks she’s a boy. (There’s also a sequel, Rick, with a cameo from Melissa)
The Witch King and The Fae Keeper by HE Edgmon - the protagonist is a transmale witch who grew up among the fae, who consider witches to be beneath them, and was betrothed to the fae prince. This is an amazing duology that I highly recommend.
The Order of the Pure Moon Reflected on Water by Zen Cho - one of the characters is transmale, but I don’t remember if it was the protagonist or not.
Anna on the Edge by A. J. Sass - a MG book about a young figure skater who knows she’s different but not really why. She meets a transboy while helping teach a skating class one day and begins to explore the language for her identity.
The Witch Boy by Molly Knox Ostertag - a graphic novel about a boy who knows he’s a witch even though males are supposed to ve shifters and females are supposed to be witches.
Nothing Ever Happens Here by Sarah Hagger-Holt - mc is a middle school girl who is a middle child. Her father comes out as transfemale and most of the story is about the family adjusting to the new identity. There is some misgendering, but it’s not malicious and is authentic on how those conversations could go.
The Greatest Superpower by Alex Sanchez - mc is a one of twin males whose parents reveal at the beginning that they’re getting divorced because his dad is transfemale and cannot live a lie anymore. A wonderful story about a family navigating a tough situation.
The Pants Project by Cat Clarke - Protagonist is a middle school transmale who hasn’t come out to anyone, and who will be going to a new school with a uniform that says girls must wear skirts. While he tries to figure out a way around the rule, the principal refuses. So, he challenges the validity rule to try and get it changed
I’m sure there are lots more, but these are the ones that I can remember having read in recent months, and I enjoyed them all.
