"The only exception to the foregoing is scripts and code downloaded and run by Apple's built-in WebKit framework or JavascriptCore, provided that such scripts and code do not 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."
Sure, but this is a case of the letter versus the spirit - and as a blatant end-run around the app store application process (they advertise it as a feature) I don't see those terms lasting too long. And/or any app that changes too much stuff on download will get pulled very quickly.
Apple don't have a track record of interpreting their terms particularly generously.
"..and code do not 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."
That seems to be a reasonable clause, and should actually benefit everyone, provided the developers stick to the rule and don't abuse that option.
Reading through their page, it gives the impression that they fully intend for people to use it for adding/changing features. The guidelines explicitly state this is not allowed.
"The only exception to the foregoing is scripts and code downloaded and run by Apple's built-in WebKit framework or JavascriptCore, provided that such scripts and code do not 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."