My Honda Element and its predecessor, the Honda CRV, are good bike haulers. The cf bike goes in without removing the wheel. It is great having the bike inside the vehicle to protect it from weather and theft. A lot of my rides occur directly after work; other rides include a post-ride meal stop or errands on the way home.
The cf frame will be fine suspended from the top tube.
If you are in a car wreck, bad things can happen to you and your bike no matter how you're set up to carry the bike. I avoid hauling the bike around with the car if I don't plan to ride that day.
With the CRV, I folded down the back seat and put a large piece of cardboard (leftover bike box from the LBS) to slide the bike over to avoid snagging/soiling the upholstery. If I needed to carry two bikes, I would put the cardboard atop the first bike to avoid entanglement and just stack them up.
Now that I have the Element, I removed one of the back seats and folded up the other.
I put a blanket down in the back and have a pool noodle in to prop under the bike to keep it from bouncing and sliding around.
If I am making a longer trip (and need more cargo carrying), I will bungee the bike into an upright position from a clothes rack mounted just under the roof.
I figure I could fit 3 bikes in easily and be able to use one of the back seats for unplanned SAG service.
If I get in the habit, I can buy a skewer-style truck mount and fasten it to a "bike board" with a separate fork-style mount for carrying the wheel. The entire bike board can slide in and out of the cargo area.
If I need to get a new motor vehicle, I'll take a long look at the Transit van. Narrow with great headroom, and a little longer so the bike will easily ride without having to tilt the front wheel to one side.