The item that's being scanned in and out of the Amazon warehouse is the box of boxes, not the granola.

This will lead to the inventory of granola to be out of sync with the actual amount at the warehouse, but in that case I'm assuming Amazon would eat the cost since they're the ones that "lost" the missing inventory. Think about a physical store. If they lose some of their inventory, it's the store's problem, not the product's.