First: «Apple eventually failed to keep Adobe Flash from its devices»
Then: «we would argue … that Apple will continue to hold this type of dominance for some time to come, and will remain the comfortable market leader for the next five years.»
Apple failed to keep Flash off? iOS still doesn't have Flash, thank God, while you yourself say Apple will be out front for 5 years anyway. Your article contradicts itself.
The only thing keeping Flash off Apple devices is Adobe. As long as Adobe continues to foist a sub-par port on OSX, making fans spin up even on modern dual-core MacBooks, Apple will continue to keep Flash off iOS for the sake of battery life and overheating protection.
To the point of the article: the Kindle app switches to Safari to get to the store on Amazon, thus following Apple's guidelines to the letter. Purchases aren't being done in-*app* here, a loophole that may or may not be closed in the near future. If you buy a Kindle book using your computer (or your Kindle, or by starting Safari yourself on iOS), you can send it to the Kindle app without Apple taking a cut — and Apple can't do a thing about it unless they want to selectively block downloads, and I don't think that's likely.
The Kindle proper is a better ebook reader anyway. I can read in peace, without everyone else in the house wanting to borrow it.