It seems to me that the aerodynamic picture of an F1 car would also have to account for all the air getting sucked into the engine and blown out the exhaust, no?
In a similar vein I remember reading that one of the reasons for the CFD restrictions was because the bigger teams were starting to spend a lot of money modelling the aerodynamics of the tyres as they oscillated in corners (because F1 tyres have a relatively high sidewall they deform a lot through corners, then if a wheel lifts a little e.g. bouncing over a curb, then the whole tyre starts oscillating laterally.) Sounds very interesting but a bit of a CFD nightmare!