Mary,
My 2 cents...
I'm don't think that either way would result in significant fuel differences. I don't think the boat makes much of a clean entry through the air....wouldn't it mostly be living in the eddy of the car?
As far as buffeting, I do think that going stern first would have less working back and forth. Since the sterns are closer to the beams, it gives the airflow less leverage to work with.
Jeff.