EDIT: One of my viewers contacted someone at Kraft for me....here is there response:
The red tape signifies the end of the packaging material and that the machine/assembly needs to stop so that the material can be switched out to new packaging. Typically, the pouch with the red stripe on it is removed automatically. There is a possibility that one of those unsealed pouches gets into a box of mac n cheese. If the consumer receives one of these pouches in their box, they must call the 800 phone number on the box to get a refund of their purchase and a coupon for a free replacement. It is advised that the consumer does not consume the product as the pouch is not properly sealed.