In brief
The extra load on the roof changes the air resistance. One test rate doesn't describe every box and every car.
Useful to know
Roofing luggage increases air resistance and can worsen the consumption. FuelEconomy.gov separates this effect from the added weight itself and describes tests with a specific vehicle and cargo set. [1]
This is a reason not to take one percent as permanent for all boxing. Size, shape and speed matter. The source explicitly notes that other shapes and sizes may give a different result. [1]
Practically in personal expense records, note whether the box is installed, whether it is loaded and what the route is. Don't compare a city trip without it to a highway trip with it, and don't attribute all the difference to one factor.
When not needed, removing the additional equipment can avoid unnecessary resistance. For installation, load capacity and restrictions, follow the documentation of the car, the porters and the box instead of taking them out of a general explanation for aerodynamics.
Sources
For further detail and to check the information: