Amazon wanted the savings of commingling without the expense and investment in proper systems for it. For accurate accounting of the source of a piece of commingled inventory, you need sku-level inventories with unit-level accounting. This is expensive, because it means each unit needs to be individually marked (e.g. a sticker with a unique ID number) upon receipt, which is more labor intensive than just counting them and sticking them on a shelf.

Amazon's sku and bin level accounting works perfectly fine for items that have a single origin. Shoehorning commingled inventory into that same system doesn't work. It was reckless, and they should bear the punative cost for its results.