Interesting question. I’m going to guess the roof box will generate more drag. There is a lot more surface area on a roof box, also you get a lot more wetted area (i.e. surface area exposed to the airflow), so the coefficient of drag, I would think, would be worse, so combined with the higher frontal area, so I’m guessing overall drag would be worse.
The turbulence generated around the frame of a bike would be taken into account in its coefficient of drag. But the effects of the turbulence might not be as detrimental as you’d think. Look at F1 cars. A following car drafting a leading car in its turbulence generates significantly less drag that the leading car. So in a similar way the turbulence generated by the handlebars, front wheel and down tube washing out in front of the seat tube, seat stay and saddle might actually reduce the drag generated by the seat tube, seat stay and saddle, and so on with the rear seat stays and rear wheel.
Difficult to say if you don’t know the numbers.