As someone early in the process who is still far from passing, it was so sad to be misgendered in this game too! :( Eventually I got ending 2, then even ending 3! I hope I experience those endings in real life one day! :)
I am sorry about it hurting. I tried to make the game as gentle as possible because being misgendered hurts. It has always hurt me and it probably always will on different levels of sting. I have days where I experience all of the different endings and I think many trans people will go through that too. I am still glad I got to transition and I hope that your transition brings you whatever you are seeking too.
Good luck and I hope when I finish my next game you consider stopping by again.