Basically you want to go fast with a big draggy box on your roof. IMHO you've created a worse case scenario for FE. You're going to take a hit no matter what car-top carrier you choose.
As far as FE goes weight is a dominant factor in stop and go city driving, while high speed cruising is mostly about clean aerodynamics and restraint on the go pedal. Hopefully you can quickly detach the carrier off the vehicle when it's not needed.
As a personal object lesson, I had a VW diesel a few years ago and used a ski rack for obvious reasons. At 70 MPH it knocked almost 25% of my FE, so it stayed off the vehicle until needed. Live and learn.
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