I think the bag tag from the gate agent is like a boarding pass. Printing it out is one thing, scanning it as you board is another. The bag tag is like the boarding pass but it is scanned by the bag loaders with their hand-held scanner. So it isn't in the system to track separately unless the the rampers have scanned it. Until then, it's a bag that went through security like any other carry on. Taking it onto the aircraft is no big deal IMO.