Apple's argument is actually very different. What Apple is saying is that the developers do not actually do anything that is covered by the patent.
Let's say I write an application that takes your photos, your address, and your credit card number, and sends them to Kodak, which will then print the photos, send them to your address, and bill your credit card. And someone claims that Kodak is printing these photos in a way that infringes on their patent. Then it is clear that _I_ don't do anything that infringes, because I don't do the printing. So it doesn't matter whether the patent is valid, whether Kodak infringes on it, or whether they have a license, and whether that license would cover me: I don't infringe on the patent, so I cannot be sued.
Or lets say I write an application that takes the music that you ripped from LPs, uploads it to a third party cloud service, which removes all the noise and jitter and whatever and sends the music back in perfect quality. If that cloud service is infringing on some patent, that's not my business, because I am not the infringer.
And Apple says the same thing. The actions that are allegedly infringing are all performed by Apple, and not performed by the developer. Therefore the developer cannot possibly be infringing and doesn't need a license, and doesn't need to be covered by any license that Apple might have.