When the Apple App Store first came out there was no in app purchases. Amazon already had a payment infrastructure so when they released the free Kindle app on iOS it used the Amazon payment system. Apple later added in app purchases and changed the contract terms (as the were allowed to do) to require all apps to only use the App Store for IAP, they allowed Kindle to remain unchanged. The exception as just not forcing Amazon to change their app.

It was allowed under the old rules, then the rules changed, then the Amazon ad these emails were referencing game out. So at the point of these email the Kindle app was out of compliance with the App Store rules, but Apple was allowing it as an exception because they viewed it as a promotion of Apple products. This ad changed their view and now though that the Kindle app on iOS was a promotion of how easy it was to move to Android.