There goes my mod points.
Amazon has two different ways the 3rd party inventory is stored in prime warehouse: with original UPC, or with seller specific code.
If the item is brand new, and has only one listing per that UPC, the seller has the option not to include a second bar code, and use the product's own UPC. (This would include most flash drives that you've mentioned). However I'm not sure Amazon will have an exact way to distinguish inventory between sellers when this is done. But even then the mixups should be very rare.
On the other hand, if the item is used, refurbished, or has multiple sellers, or the seller chooses to do so, they will use a second bar code, specific to that seller, and they should not be easily mixed.
Yes, you'll have better inventory control if you're buying used from Amazon.