Punkzilla isn't just the book's title, it's also Jamie's nickname. He tells us:
Somehow Fat Larkin knew about my musical taste probably because I was always talking about punk rock. He even started calling me Punkzilla which everyone in Portland called me too. (1.25)
Jamie is an androgynous name, and Jamie's not a fan of being androgynous; Punkzilla is way more butch. Sometimes he just goes by Zilla—this is how he signs his letter to Albertina—which underlines the fact that his nickname is a shout-out to one of the most legendary monsters of all time, Godzilla. Yeah, so tough.
The title then, refers to Jamie as well as who he wants to be—and is—in the world. After all, dude definitely loves punk music, even if he's softer than he wishes the world recognized.