As is often the case, it's the perfect intersection of corporate greed, bored engineers with a NIH syndrome and device limitations
The article ends with a discussion of Calibre. It would also be very interesting to know how much Calibre is used with pirated books.
Amazon must be following an interesting dance with copyright, piracy and the Kindle. They know if it gets too out of hand that's the end. But if they were to entirely lock down the Kindle to anything without DRM they would also know that many people would shift devices.
The objective of antipiracy restrictions shouldn't be to restrict the top 5% of most technical power users. That takes far too much time and effort, and frankly power users provide word of mouth recommendations.
The objective of antipiracy restrictions is to stop 95% of users going to the trouble of piracy.
This obviously feels very sketchy, not only because you might be including Amazon in some very transparent piracy, but because it works TOO well. By which I mean, these files aren't simply added to your device, but to your Amazon library; these are then readily available OTA to all devices you own and any you add later.
I wonder if the difference is that with the exception of comic books (sigh), most ebooks are small enough that they download quickly, yet have good metadata and often excellent cover art, so they replicate quickly. And they rarely get buried inside of unnecessary folders the way other files do.
It'd be pretty awesome if say, you could visit Humble Bundle and after buying a DRM-free collection of ebooks, just hit a button to transfer the entire bundle to a Google Drive folder or iCloud Drive folder without having to download and upload things. That's still maybe a missing thing. But it's not terrible to have to send files manually. It's just extra work. (How lazy can I get, apparently?)
I don't mind paying $15 for a book if the author(s) are paid well.
I don't see how Amazon could know for sure. I have never uploaded a pirated book to my Kindles, but have uploaded dozens of books via Calibre, either public library books that aren't available in native Kindle format for some reason, or obtained elsewhere (notably Tor.com's regular offers of free ebooks).