Do you mean that you want them to know that they're trans before the story?
For that, I would recommend "Fire Burning" by bafflinghaze. It's an action-oriented BL about a trans man who's roped into being the body double/replacement for a noble mage in a battle academy. It's short, already complete, and all the characters are extremely loveable. I left a review on the novel itself if you'd like more information.
You can find it here:
https://www.scribblehub.com/series/160447/fire-burning/
Their short GL story, "Blooming Flowers Of My Heart", also fits. It's a sweet little romance story that you can find here:
https://www.scribblehub.com/series/175335/blooming-flowers-of-my-heart/
There's technically also my short story "Petrosinella, the Perfect Witch's Daughter", but that's a comedy revenge tale where the MC never had any problems with her identity and is setting out to troll those who do. Not necessarily heartwarming. (It's also GL, in case that's not your thing.)
You can find it here if it does interest you:
https://www.scribblehub.com/read/22...wheel-a-yuri-garden-anthology/chapter/225130/
If you're alright with small parts of the story being set before the MC realises they're trans, then I highly recommend "The Glory of Bowsette" by Thedude3445. It's Mario fanfiction of Bowsette, but it's actually a very gripping action/adventure story, with a clever use of Mario lore and comedy. This is a GL where the pairing is Peach x Bowsette.
It can be found here:
https://www.scribblehub.com/series/124048/the-glory-of-bowsette/