Phil made it sound like he didn't like the ad, but the reason for the removal of the exception was that Amazon was advertising that people could buy books from their phones, clearly promoting the phone-first use case.
If you have any business understanding that you should understand that no business is a charity: neither Amazon nor Apple. Any money left on the table is just free money for the shareholders of another company.
They made the point that Apple devices were more popular than Kindle, implying that Amazon was basically using Apple devices for lead-gen for book sales without paying Apple their cut. Their original deal was that Kindle was supposed to be a device where you bought the books, and you could just read them through the phone app as a convenience. Since the primary use case shifted they began enforcing that fee.
This seems to be a consistent app store policy, however it's been spun over the years.