I think this could make a great story, overlooking the slow physical aspects of transitioning, and focussing on the way it is perceived in the wizzarding world.

Imagine it, in the first act the character is introduced, and plans to steal ingredients for a potion from Snape's lab.

Act 2, the character is caught, and brought to Dumbledore's office to explain their attempted theft. Dumbledore then calmly takes the matter from Snape's hands and properly talks to the student, as they explain themselves.

Act 3, character given weekly doses of a potion that will slowly reverse their gender, given to them weekly by a sneering Snape under Dumbledore's orders. This could be used to explore gate keeping and institutionalised trans phobia.

Act 4, character is under a charm to appear as their former selves to students until they are comfortable. Character adjusts to physical changes, slowly grows to accept self and grows to resent the charm.

Act 5, big trouble, events at the school lead to the character losing the charm concealing their appearance in public. Ridiculed for the act, and either avoided or abused by pupils, the character loses their progress, slipping into a depression and avoiding contact with students. Maybe they even cease taking their weekly potion. (I like the idea of Snape coming and telling the to character drink the potion, then pouring it down the drain in front of them. The character's reaction, and Snape's future actions could massively advance the emotional state of the story)

Act 6, the character is forced into confrontation, and barely emerges, hurt both emotionally and physically. The character learns to accept self, and confronts Snape, resuming their potion usage.

(I like the idea of Snape having kept a cupboard of them spare)

Ok, I may have gone a bit overboard here, but I really like this idea.