It will add a cookie (lexical-binding) to the top of the file. If you want to do it manually put this:
;; -*- lexical-binding: nil; -*-
or this:
;; -*- lexical-binding: t; -*-
at the top of your custom.el file. They want it to be explicit now because eventually lexical will be the default. If you put in the former then when lexical becomes the default, the file will still use the current dynamic bindings. And if you use the latter, if there are issues you'll discover them now before the default changes and you're surprised by it.
