[Not a pilot] Perhaps the question I should have asked is, do we know the actual pounds of fuel / passenger actually experienced by the operators of the two different airplanes?
I ask about the A380 because the greater fuel consumption was to be offset by carrying more passengers per trip. I'm wondering if B747 operators can round up ~400 passengers more often than A380 customers can round up ~500 passengers.
To answer your good point that B747s could be flying with empty seats, too, my thought was that it would be more likely that the larger capacity airplane would fly with empty seats than that the smaller capacity plane would.
If there is a passenger preference for a twenty-first century design over a 1960s plane, then perhaps there may be more empty seats on the older plane.