Personally, I find rape-as-comedy - difficult and awful as that is - to be less tired and easier to make work than rape-as-serious-drama. Not to say I'm a fan of either. And for the record (TW to end of paragraph) no it does not take penetration to make a rape.
Probably my favorite queer-teen-character-populated story of the moment is Jocelyn Samara's
Rain. Notable for just how little "sex and/or homosex" (

) happens, even off the page.
Just to throw an idea out - brainstorming style - what would it feel like to grow up TS in an extremely supportive environment, as a happy "girl-with-a-penis" and then one day ask, "So, Mom, when are my breasts going to grow?" I think backstory moments like that might just manage to sell the early-HRT story.
Because now the story can be a little less about ooh-she's-
trans and a little more about something universal: leaving the nest for a less sheltered real world. And, with a twist like that, it's okay to use a somewhat tired plot, like "girl gets boy" a la every Disney-channel pre-teen chickflick of the past decade.
Of course, you'll want to keep looking for twists and ways to make it authentic. It's a skeleton, build on it.
Actually, not entirely related, but I'm going to spring a bit of a trick on my
mmm, on my family. We'll just say they're awkwardly traditional. They don't get any of this trans-ish-stuff, and me being non-binary dosen't make it any easier. Well, I've suggested Mamoru Hosoda's
Wolf Children as a Thanksgiving-day movie. It's not actually about trans issues. Not
directly.
Hana, ore ga nani ni mieru? - Hana, what do you see me as?
And then living stealth at school, and Yuki and Ame's struggles with identity as they grow up...
Sure, not
directly.
My point is allegory is a perfectly valid way to say something artistically. And it might make it easier to get past preconceptions and prejudices that way. Maybe not helpful for you current project, but something to keep in the back of your mind.