I'm going to agree, you're looking at a combination of the added drag from the top box, a little more air flow from the exhaust, but probably a significant factor is that the devil whispering in your ear through the sound of the engine has gotten louder...
When the exhaust system on my old pickup "fell off" (what are the odds that of hitting a reciprocating saw and it cutting off your exhaust system one sunday afternoon?) and was replaced with a cherry bomb glass pack, my gas mileage mysteriously went down about 3 mpg, but then over the next few months slowly increased up to 1 mpg better than before.
My theory was that with the new exhaust, which wasn't much louder but about 90% more bad-ass sounding, when I shiftered I had a tendency to not let off on the gas as quickly when I pushed in the clutch, so then the engine went 'vaaarooooom pop pop pop...'
But after a couple months, I got used to the cooler sound and did that far less often.