Back to Heartstopper (sorry!) -
If you watched the show a little more carefully you'd see there are various references to things not always being smooth. For instance, the teacher who refused to call her Elle, the fact she became friends with Charlie while they were both hiding from homophobic and transphobic bullies in the art classroom the previous year, and Harry is specifically named as a transphobic bully.
Haven’t watched, but it sounds like this is all from Elle’s perspective coming in thinking "I want to go to the girls' school" and offering examples where the people opposed to Elle's way of thinking are kind of straw villains - everyone knows bullying is wrong, and it's silly to refuse to a call a pupil by a nickname. What people are wanting in addition is some critique/examination of the impact of the school effectively becoming mixed sex: how it's possible, the reasons behind the push for it, pros and cons, how the change impacts others, the reasons there might be resistance, how people with differing perspectives might come to understand each other. (E.g., does Elle's viewpoint change at all? Her friends' viewpoints?)
Different situation, but something a bit like this was done well in the US teen drama Switched at Birth. Daphne’s family moves next door to Bay’s in the first episode so family/home drama is combined, but there are parallel story lines for anything involving the girls’ schools, friendship groups, etc. This gets resolved by Bay becoming dissatisfied with her elitist, conservative private day school at the same time Daphne’s state-funded school for the deaf approves a pilot program for hearing students. Bay switches schools, and several of her friends follow the next semester/year.
Adding hearing students causes problems and conflict - some predictable, some not. While it’s just one aspect of the story - we've still got story lines for Toby, Kathryn, Regina, John, and Adriana going on in the same episodes - we get a lot of perspectives from deaf students initially closed to any suggestion of integration and deaf students welcoming it, and from hearing students upset at the pushback and hearing students sympathetic about impacts they didn't anticipate and even questioning whether they should be there. There’s also a good examination of the political economic context: less funding and support for special programs even when proved to be needed and effective, more for generic “education” for everybody.
In Switched, because we know the characters and are sympathetic to them, the whole range of opinion and perspective gets fairly considered. Even where things happen that we all know are negative and wrong - e.g., attacking individual students rather than focusing on the policy - we see WHY that can happen. In the case of Heartstopper (just for example) you could have a sympathetic character with a backstory of sexual assault and rape trauma syndrome, or a sympathetic Muslim character who decides to leave the school (or her parents pull her out) because it’s not single sex, or a sympathetic teacher reflecting on the history of same sex schools and what's lost if they go.
I agree, though, that Heartstopper may not be the right vehicle for this kind of treatment as (based on the comics) Elle is a minor character and the overall tone is upbeat and kind of fluffy/slice of life - more an LGBT+ Wonder Years than hard-hitting social commentary or problem-driven plotting. (Maybe a spin-off, or an opportunity for another aspiring show runner?)
Though I imagine you'll implode when, as happens in later webcomics, Elle starts going out with Tao, who is straight. Sexual orientation isn’t the same thing as being or not being trans. Trans people can date anyone, and anyone can date a trans person (usual caveats on mutual interest and consent apply).