Paternalistic tone or not, the checkin agent was trying to make the line go faster. There's always some person who doesn't believe in using Easy Chicken (probably the same type of person who doesn't believe in the concept of an electronic ticket).

re: VDB list on the connecting flight
If you were making a sameday connection, I would think that the flight was under airport control from wherever it was departing. Thus, you couldn't get on the VDB list until you arrived at the connection city.. right ?