I'd say it explains the decrease you're seeing. I would still bet the roof mount approach would be worse though. You could pretty easily test which is better by doing a coast down test to compare them.
My thoughts are:
1) Make/modify/get a cargo rack for your camping gear to go behind the car instead of the bikes. Cram the bikes in the trunk and close it. The gear could be packed more densely and closer to the rear of the car, which is good.
2) Much harder, but more fun: fabricate some kind of aerodynamic shape that will fill/sit in the void between the rear of the roof arching down to the high part of the trunk lid (when it's in that partially open position, with bikes sticking out). Such a mod may even be favourable for approaching an ideal streamled shape depending on the height of that open trunk. Dealing with side taper from the C-pillar back to the open trunk lid will be trickier though.
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