I don't think there will be a clear roof vs. trunk recommendation as both systems have their pros and cons:
- Does not cover the trunk lid (access to the trunk when fully loaded)
- Bikes stay cleaner (Especially when raining - on the trunk, the rear of the car sucks up road grim which gets into the bikes moving parts)
- You have to lift the bikes up to the roof for mounting (more or less difficult depending on your size and roof height)
- Significantly changes the car's steering and wind behaviour
- Higher wind resistance, therefore higher fuel consumption
- Risk of driving under a low object and significantly damaging bike and car (Putting a small sticker on the top of the windscreen in front of the driver - I use a red arrow - meaning "Bikes on roof")
- Lower wind resistance, therefore less influence on steering and fuel consumption (With modern cars such as the Mazda 3, this is surprisingly significant)
- Loading/unloading is easier
- Can see if bikes become insecure
- Maybe prevents access to the trunk when fully loaded (may depend on car and rack model)
- Influences sight through rear mirror
- Blocks rear lights and number plate (Legal considerations in most countries)
- Bikes more prone to damage - Major : accident, dragging on ground, Cosmetic: rack design.
For the scratches: the roof mounted one has the advantage of using points on the car that are dedicated to mounting, which means that there's very low danger of scratching your car (as long as you are careful when mounting the rack itself). The trunk mounted racks normally have some foam rubber on their fastening parts, which normally also prevent the car from scratches. So here, there's also normally no problem.
As long as you don't buy the next best cheap rack but have a look at some tests and invest a bit more money, both types will do their job. Also, as long as they have a reasonable mounting design (that is understood and used correctly), highway speeds (130km/h, 80mph) shouldn't be a problem with any of them. On the other hand, both types can be dangerous if the bikes are not properly fastened on the rack. As far as I know, the German technical control board (TÜV) and automobile clubs recommend the trunk version over the roof mounted one where possible, because of their lower influence on the steering of the car.