Correct me if I am totally wrong here, but isn't the issue not with introducing new private frameworks or exposing new methods but with changing the behavior of the interpreted code that interacts with already exposed frameworks/methods? The relevant language seems to suggest that you could still be in violation of Apple's TOS if your script(s):

>change the primary purpose of the Application by providing features or functionality that are inconsistent with the intended and advertised purpose of the Application as submitted to the App Store.