I use magnetic lights for towing our Ford Fusion hybrid. Reasons being:
1. I don't want to tap into a hybrid's (extremely complicated!) electrical system any more than is absolutely necessary.
2. Trying to keep toad wiring simple, generic, and transferable. Hate spending tons of $$ on wiring tail-lights, only to have to do it all over again and spend the $$ all over again when trading vehicles.
..That said, your dealer was right - Magnetic lights can and do scratch paint if any dirt gets between the magnet and your paint. Wiping the surfaces off real good before putting them on as well as using small pieces of window tint material (as already noted) or other thin cloth will minimize that risk.
Or, you might be able to do what I'm doing: Mount the magnetic lights INSIDE The car, up against the back window. All I had to do was put velcro on the bottom of my magnetic lights, and they stick in place easily on the 'shelf' behind the rear seats. They sit right behind the headrest on the rear seats out of the way (and do not block your view). Never have to take them off if I don't want to, as they stay in place fine and aren't in the way or cause any problem when driving the toad. Never have to worry about scratching paint again. :)
As to the wiring for magnetic lights: As already said, do NOT even THINK about running a wire along outside of vehicle, where it will be up against the paint!! That WILL cause bad scratching (don't ask how I know, haha). Route the wires underneath the car somehow, come out in the back near where you will use the magnetic lights. I actually had U-haul do that wiring, as I was/am too fat and lazy to crawl under the car and do that, haha. I just asked them to run a standard '4 flat' wires from the 6-round connector I already had up front on the base plate, and come out with it in the trunk where I'd plug in the magnetic lights. They did it for just 1/2 hour labor, around $37 IIRC.
I do have to confess, though, that one day I probably will break down and get a custom tail-light wiring kit like
THIS one and put it in, and stop using magnetic lights. Only way I'd do it is with a kit that uses OEM specific wire harnesses (no wire tapping necessary).