Yes, Amazon definitely has a counterfeit problem. But that's not a problem with the buy box.
If it were, then Amazon could say to publishers, "We fixed the counterfeit book problem, now customers have to click on another link to buy fakes from third party sellers." But putting counterfeits 2 clicks away instead of one click away isn't actually a solution.
There's a lot to criticize Amazon for. I just thought the linked Vox article was incredibly terrible reporting.