Yep, the dealer probably made more money adding a vinyl roof to a car than ordering a vinyl roof from the factory.
Mopar Collectors Guide did a couple features on dealer-added vinyl tops on the 1969 Dodge Charger Daytonas. In that case, I'd think it would be a unique and probably value adding feature if verified done when new.
It would be a tougher call on your car, but removing it might mean you end up painting the whole car.