The fact that their example includes using cljsjs package for externs is troubling. For the meanwhile, to avoid worrying about extern files, I'd stick to using a separate build process for npm packages.
Yeah, but without externs this breaks on advanced compilation, right? So, while using webpack to bundle npm deps is a good idea (that might also get unnecessary in the future with things like node module resolution landing in cljs compiler), you still need externs for the functions you're going to call from your cljs code. Luckily the latest cljs compiler will help you get those right.