Basic aerodynamics, as I remember it from many years ago, would say the only one of those options that would be different from the others would be the front wheel off, but as to whether that would be worse or better I don't know.
With the bike angled down, the seat may have greater drag, and the top tube is no longer horizontal so my guess would be that having the frame horizontal is best (it has been designed to have lowest drag in this position with a rider so this seems reasonable)
As to where on the roof the bikes should be, the most significant drag is from the airflow heading from front to back of the car. There is a minor effect over the edges of the car, but it isn't going to make a noticeable difference, so my guidance:
Don't worry about the drag, and secure the bikes where you can make sure they aren't loose and can get them up and down without straining.