What's the deal with the single-type-of-piece bags on Amazon?
I think it's really hard to tell for sure without actually making a couple of orders and seeing what arrives. What I can say is that it appears that they are selling at a HUGE markup over similar parts available on Bricklink. (A quick check shows an average markup of 600% over BL on several lots)
I would guess that either the first, third, or some combination of those two guesses is likely to be the case here. Since secondary markets like BrickLink and BrickOwl are somewhat niche sites maybe the seller(s) are taking advantage of people unaware of them and selling at a very good profit to a larger market. Additionally since Ali Baba, Ebay, and Amazon tend to have a large number of counterfeit sets available these sellers may be able to get away with selling all or a mixture of counterfeit parts to increase their margins.
As for your second guess, there are programs that The LEGO Group makes available to organizations of various sorts to acquire large numbers of pieces at fairly reasonable prices however they do tend to monitor the secondary market fairly closely for evidence the parts from those programs are being resold so, while certainly still possible, it is less likely the parts are being sourced that way.
Again though, it is nearly impossible to tell simply from the advertised lots without actually making a purchase to verify what you would get.