As far as stuff where it came out later that a character was canonically TG, one of the only examples I can think of off the top of my head is the game Celeste -- the creator of it began transitioning after creating the game, and she's said that while she was actively Not Thinking of it at the time of making the game, the game itself is a sort of chronicle of her own struggles, and that as far as she's concerned the main character is, canonically, a transgirl.

Melanie E.