I did several trips (New Orleans to Flagstaff,AZ) with stuff(including bikes) on the roof vs suspended from a hitch rack. NEVER PUT ANYTHING ON THE ROOF.
I got 15.9 mpg VS 22.25 MPG .This was 2 3000 mile trips with both methods.
Inside or tuck it in behind the vehicle.Luck,Charlie
PS I'm about to find out how badly a "trunk rack" kills mpg on the Prius(same trip).
PPS On a trip without any racks, I got 24mpg, but the trip was different in other respects, so the extra 1.75 mpg might not be because of no hitch rack.The hitch rack will cost something MPG wise, but the 1.75 mpg would be about .2 gallons per hour at 66 miles per hour. Seems a little high.