Nailed it. Sex ed is differentiated by sex because puberty is differentiated by sex (and different sexes also experience different things during sex and have different concerns!).
My understand is also that "boy sex ed" consists of a lot of talking about male puberty and things like wet dreams and surprise boners and whatnot, which obviously no boy is going to want to talk about in front of girls. Shame is extremely damaging in these kinds of environments, it prevents kids from paying attention and learning stuff that's important for their future health and safety.
Like, do I agree that things like safe gay and lesbian sex should be addressed during sex ed classes? Absolutely. Everyone should learn how to have safe, healthy sex, and there are particular concerns that should be addressed for gay and lesbian students. But it would never take up anywhere near as much time as, say, puberty or even heterosexual sex (because that's the kind of sex most people will have).
And trans shit should have nothing to do with it, because that has nothing to do with puberty or sex. Though I guess the teacher could point out any trans students and make sure everyone knows that they'll never go through normal puberty (because puberty blockers), will be completely infertile, and nobody will ever want to have sex with them, before they make them sit out the class to ensure that they're not "misgendered" by being put in the class of their sex and that they don't make students of the opposite sex uncomfortable by invading theirs.