Take both wheels out & flip them upside down. Put them in with one facing forward (handlebars behind front seat), and one facing backwards (rear DR near front seat). Scoot them as close together as you can on one side of the car and use the space between/around the bikes as packing area for smaller items.
I've scotchguarded the back of my seats and my interior roof so if I have any inadvertent chain-upholstery contact, the grease is easily removed with some upholstery cleaner.
And yes, nowhere in a car is totally secure. We mainly put them in there b/c it was storming like crazy on the way home from the race we were at.