Instapaper Pro 2.1 was just approved, I was able to generate a promo code, and an internet friend was able to use it to install the app for the first time.
Curiously, it did not pop up any warning dialogs.
So I can confirm that this App Store problem has been fixed. To the best of my knowledge, revealing this information doesn’t violate any part of the NDAs or Terms. If I’m wrong, I’m sorry, and I’ll take it down.