So Topa realizes something is off and feels like he's different, finds out he was born a girl and transitioned into a boy and wants to be changed back, political obstacles prevent it, but they find a loophole against Klyden's wishes.

Given the real world discussion about transitioning young kids, I have to say I think they threaded the needle with this episode, but ONLY because Topa had been surgically altered as a baby which any sane person would see as wrong, so switching him back to a her made the most sense. I think it could be read as how doing unnecessary surgeries on children is wrong.

However, I think this could very easily be interpreted in the opposite way too. You have a scene where a child sneaks off to get a secret surgery by someone who's not a licensed doctor and that person assaulting the child's parent when they try to intervene. But again, given they did this to Topa as a baby and Klyden has been an unlikeable douche through the entire show, we of course are going to side with Topa's choice. It's sort of like a reverse David Reimer.