As you say, Amazon was able to identify the merchant specifically but wasn't able to determine whether the goods are genuine. If the goods weren't comingled, this would be less Amazon's problem and the goods wouldn't be in Amazon's warehouse so at least the seller would still have his inventory if Amazon blocks his products.
Comingled doesn't mean that they just bunch them all up in some bin and then can't tell which is which and where they were from. It means that if some warehouse closer to the buyer has a similar item, they'll ship that one, because shipping will be cheaper and faster coming from the closest fulfilment center.
If Amazon didn’t offer fulfillment as a service, and just bought product from suppliers to sell, this same issue can arise - the supplier can deliver items which seem possibly fraudulent. Then Amazon will fight with the supplier about returning those items and depending on what kind of contracts are in place, could end up destroying them (this seems to be essentially what happened here).