It's all about aero drag. Hatchbacks have some of the worst aero of any vehicle, in terms of lift. They are notorious for excessive and even dangerous amounts of rear lift. The early New Beetle and Audi TT were famous for losing control on the autobahn because of excessive aero lift. The fix was a rear spoiler as standard. It creates drag which reduces lift. The same applies to the Fiesta hatchback. Egg shaped cars have tremendous aero lift so they add the rear spoiler to help counter it. Instead of reducing net lift by increasing downforce, they simply create drag and achieve the same result.
Back to the mysterious case of cars increasing mpg when adding a rooftop cargo box: anything that cleans up the aero profile over the vehicle will reduce drag and increase efficiency. Cargo box designers put great effort into designing their products as slippery as possible. By accelerating the air going under the box, it pulls air away from the rear spoiler/hatch and effectively reduces overall drag. It is definitely an exception, but it does happen.
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