Hi, Efi! I'm yet to make a game with TG content, but my novelette Little Magic features a gender-ambiguous protagonist, which becomes an issue repeatedly throughout. Their actual gender is never revealed, though my readers were able to guess easily. (The protagonist is cisgender, just doesn't like to lean one way or the other.) Would that fit the bill? I played with gender and gender expression in other stories, but not nearly as prominently.
That said, a friend of mine suggests http://catherine.wikia.com/wiki/Catherine_%28game%... as a game with a TG character, which tackles relationship issues. It's apparently a bit iffy in places, but largely a good effort.
Either way, hope this helps. Cheers!