Apple is saying "we're providing a value-add, pay us" but not allowing developers to price it in to their balance sheet.
You use them to advertise your site where customers can get a discount if you bail from the app store and buy from you directly. So many developers would try that oh so clever trick that they already know better in advance.
Unless you're one of the anomalies who actually does a better job at driving traffic to your apps than they can, it makes no sense to complain about this.
If you call the shop and mention using Groupon, most of the time they ask you not to purchase the Groupon. They still honor the discount, but avoid a 50% take by Groupon.
That's not true at all. In fact, Spotify did have IAP in the app, and they charged an extra $3 for it.