Do we know that Amazon doesn't comingle their "sold by amazon" stock with FBA third-party sellers? I can't see anywhere that they say they don't on some research, and it would seem to be an obvious thing to do.
Yep. They commingle because they use the UPC code as the identifying barcode for the item. If any party wants to avoid commingling, they either need to manufacture with a different barcode, or cover over the barcode with a different, vendor specific one.