The pads on a rack can dull the paint after a while. Maybe wrapping soft cloth over the pads would help, but I doubt it.

I used to fit my road bike in the (4-door) Integra trunk with the back seat up. I had to remove both wheels and the seatpost. I put a heavy blanket on top of the bike, then the wheels both fit on top of that. I used some chunks of packing foam to keep the wheels from sliding around.

With a trunk or hitch rack, make sure your wheels aren't in front of the exhaust pipe.