You'd have to ask the MIT crew for the details.... a bunch of them who were also cyclists did a number of wind tunnel tests.

One thing that they found was that if you don't have a aero seat tube (yes, one that is specifically shaped to cut through the wind - most new TT specific bikes have them these days, but many road bikes or an older TT bike will likely have a round seat tube) that having a bottle on the seat tube was more aerodynamic than having no bottle or a bottle on the downtube.

The article I read didn't go into specifics, but there are lots of things that are counter to what you might think when dealing with aerodynamics - like dimpled things are more aero - think of a golf ball. That's why the newest high end wheels you'll see are dimpled rather than smooth. I'm surprised no one has done it with a helmet yet. Maybe it would just be too much to try to convince people to wear it... But anyway, often its a bigger picture thing about creating smooth air flow and even though it seems like having a bottle in the way would create a larger area to cut through the wind, it must have some other effects on the way the air flows around the rear wheel of the bike that make it better.