I disagree with it being called an Apple premium.
Apple has a store. Amazon has a store. Who is to say that Amazon's portion of operational costs and profit isn't the premium?
Amazon could choose to have a Kindle experience which doesn't go through the App store, such as a HTML 5 app. They distribute in the store because of the discoverability (and likely because they prefer to have a native app that can enforce their store's content DRM.)
Amazon could choose to expose more functionality through their app, such as title search, being able to look at reviews, download sample chapters, and even be able to fetch new books through the kindle unlimited and other prime features. They prefer to drive everyone to their own store instead.