Here's a scenario: Provide a FREE app through the App Store, which requires an activation key to work. Charge $200 for the activation key on your own website, and Apple misses out on their cut. That is the scenario Apple is likely trying to prevent. Similarly, provide for free a game framework in the App Store, and charge $9.99 per level on another website - same deal.
On the other hand, in Cube Runner you can put in the URL for additional level packs and the game will download them. But Apple might not consider a level pack to be an additional feature or functionality - the app does the exact same thing it always has, just on a different data set. Similar to downloading new showtimes for a movie app.
Can one app read another app's data? Meaning, can level packs be bundled and sold on the App Store, to be used by a separately purchased app?