An article in Sport Rider many years ago on aerodynamics showed a larger rider actually filled the low pressure void behind the windscreen better than a smaller rider, which improved top speed.
I would suspect your reduction in top speed was due to the difference in acceleration during the length of the straight, even though your speed entering the straight was higher.
In general I agree with what your saying. In the case of a bigger more fully faired bike, where even a taller rider can tuck both knees and elbows in and get fully below the windscreen, I would agree. However the fairing on our race bike is farily small (see avatar pic) and doesn't have side fairings. The SV is not a large bike with much leg room. I can either tuck my elbows in and have my knees sticking out, or tuck my knees close to the tank and have my elbows sticking out. I can't do both LOL! Either way I'm not even close to looking through the windscreen!
Also the fuel tank on our endurance bike has been modified to carry more fuel so it is a full 1.5" taller than a stock tank, so any difference about "filling a void" behind a windscreen is diminished even more.
Although, I agree that reduced acceleration due to the weight difference is a significant portion of the difference in top speed, when looking at the speed trace it's obvious that aero is playing a signifiant roll. My teammate actually lets off the gas sooner than I and you can see he is still accelerating at 119 mph just before he lets off. On the other hand, even though I am on the gas longer, you can clearly see that my speed has come pretty close to topping out and I'm barely accelerating even though I'm still on the gas.