This is a long article that confuses the issue. The root of the problem, if it even exists, is that some sellers sell bootleg copies on Amazon. That is what the article should be about rather than the buy box.
PDFs of my Kindle version have also shown up immediately on download sites. It would not be hard to make bootleg copies on-demand, list them, and ship them to customers. Not all Amazon customers use Prime, and may be willing to wait a week or two. To get Prime status, the sellers would have to use FBA and ship inventory to Amazon.
Note that this is how every other product on Amazon works, and there have been plenty of complaints about counterfeit products: http://www.cnbc.com/2016/07/08/amazons-chinese-counterfeit-p...
If the experience of other manufacturers/brands are anything to go by (see https://news.ycombinator.com/item?id=13927641), I fear more and more pirates will get into books now that it's possible for them to own the buy box. It might not be a huge problem now, but I predict it's only a matter of time before it becomes one.