Him by Geoff Ryman. It's an alternate history story where Jesus is a Trans man.

The Seep by Chana Porter is a beautiful piece of weird sci-fi.

Model Home by Rivers Solomon. Haunted house story

Although it technically isn't explicitly about trans people, Terry Pratchett's Monstrous Regiment explores a lot of ground about repressive gender roles and norms, feminism and the arbitrariness of religious doctrine. It does all of this while being absolutely hilarious and a joy to read.

It's also technically part of a series, but like all Discworld books can absolutely be read as a standalone book.

Maybe not an absolute top pick due to not cleanly hitting all your requirements, but I'd still recommend it.

A while ago we read Pet by Awaeke Emezi in our solarpunk bookclub. The protagonist is a young trans girl. Though the book doesn't make it a big thing. Its more about finding a human monster (meaning abuser). It's a really good read and rather short (like 130 pages).

Check out Margaret Killjoy. She has written some stories. I only ever read "We Won't Be Here Tomorrow, and other short stories"

I don't think the character in her short story was trans, but it wouldn't surprise me if one of her stories are.

https://en.wikipedia.org/wiki/Margaret_Killjoy

Most Ardently by Gabe Cole Novoa. It's a retelling of Pride and Prejudice, with the twist that Elizabeth Bennet is actually a trans boy. Written by a transmasc author, too!

Recently read the convergence trilogy and one of the main characters is trans. I liked the books.

Additionally the left hand of darkness is about a planet full of genderless people that change to male/female idk if that is considered trans. The book in general is commentary on gender norms in our society. This one I think puts the most emphasis on gender of the three.

And finally one of the main characters in Robin Hobb's Realm of the elderlings series is also trans or non-binary I think. It is a great depiction of how the actions of a person are more important than their gender, but it is not the main point of the series. Still a great fantasy series I think.

P. S. Everything from Le Guin is great and I highly recommend it.

If you're okay with a graphic novel, I recommend Nimona: https://en.wikipedia.org/wiki/Nimona

Also has an animated movie adaptation.

Haven't read it myself yet, but I've heard a lot of good things about One of the Boys by Victoria Zeller.

She Who Became The Sun by Shelley Parker-Chan. It is the first book in a duology, so might not work for you.

Happened upon it via someone else here, check out Woodworking by Emily St. James

@OmegaMouse I recently read Smile As They Bow by Nu Nu Yi. It’s a Burmese book which features a trans protagonist. Really interesting read and great insight into Burmese culture too.