I was focused on the iOS app in this case study. The e-Ink Kindle devices have different constraints, use cases, and benefits.
I suspect many of the issues with the app are either intentional or not a priority for Amazon. Their top priority is to sell ebooks. I don't believe it is a good business decision or a good user experience to restrict the potential of the iOS app as a strategy to sell more e-Ink Kindles—and I also don't believe that is Amazon's intention. If they wanted to force people to buy physical Kindle devices they wouldn't have an iOS app. Their goal should be to build the best reading eco-system possible. As a Kindle reader who owns an iPhone and an e-Ink Kindle I find use cases for both and want both to be great experiences I can seamlessly switch between.
I suspect Amazon is selling e-Ink Kindles close to the cost of manufacturing. They put ads on the Kindle screensaver to reduce the price as low as they can. They are focused on driving sales of eBooks. Which was a good strategy 10 years ago when ebooks were a relatively new market but now there are readers with hundreds or thousands of books in their libraries; not designing for those influential users could lose them market share.