This is a tough one. Teen-accessible "anti-religion" books have never really been a thing. It's the religionists who like proselytising to youngsters more.
Plus, you don't really want it to necessarily be a "gender critical" thing - ie a criticism of their position (Dawkins versus religion style), rather than something expressing its own message.
But then, what is the opposite message to genderism, exactly? To some extent it's humanism - forget the bloody boxes. At the kiddie level there's Rachel Rooney's "My Body Is Me", but what's the more grown-up version of that?
And then the real male/female issues do still remain - the ones that genderism tries to obscure. Which is kind of back to criticism again, but potentially more productive than just having a go at a religion.
So one thing that springs to mind for that is Caroline Criado Perez's Invisible Women - but I confess I haven't read it myself, and don't know how accessible it is.
The thing is that genderism is kind of interesting, with its Pokémon style collection of identities, flags and rituals. Reality can be a bit mundane sometimes, until you actually dig into it. Another thought - maybe something biological? Putting humans into perspective alongside other creatures? Are there any good "Weird and Wacky Ways Animals and Plants Get It On" books to put us into perspective.
I fondly remember Emma Hilton's twitter thread. Is there a book like that?