They probably want to check anyway to see if anything else is getting low (or ran out because a note wasn't delivered) to decrease the number of restocking orders placed. The notes just help indicate when an order needs to be placed earlier than expected.
The order typically runs with not just milk but all the supplies. It's just the "going out of milk" trigger happens most frequently.
And yes, using different kinds/colors of cards for different kinds of milk might have been an improvement to consider. It would, however, make the system more complicated. Was it me, I'd start with a simpler design and iterate only when I saw the need.
It follows the rule of thumb: make it as simple as possible.
