It doesn't matter who made the device and its OS, it matters who made the user aware of the existence of the app. And I'm pretty sure that was Amazon's own marketing. Your conclusions would only hold if the user discovered the Kindle app entirely through the influence of the app store itself.
By your logic, my ISP owns my relationship to HackerNews because I used my internet connection to post this comment. Oh and Apple does too, because I'm posting this from a Mac.
It matters who made the App Store and facilitated the app in question. If more iPhone users are downloading the Kindle app than Android users by a wide margin, then that means that Apple offers a higher value to Amazon. You're oversimplifying the relationship but the fact is that Amazon's contract with Apple was based on Amazon's assertion that it would only be existing Kindle users that would want to download the Kindle app and that provided value to Apple. When that was no longer the case, the agreement ceased.
By your logic, my ISP owns my relationship to HackerNews because I used my internet connection to post this comment. Oh and Apple does too, because I'm posting this from a Mac.