I would expect more scratching from pebbles thrown up by other cars on the highway than from a magnet. Go for the wax coating option after a car wash, that will give you better results long-term than worrying about exactly one of the many ways scratches happen.

I would expect more scratching from pebbles thrown up by other cars on the highway than from a magnet, but you can't avoid these if you move your car out of the garage.

Getting a wax coating makes sense, but more than that is unlikely to be worth the money. Your car will depreciate in value whether you use it or not, and doing so while being reimbursed is the best deal you can get. Any potential buyer in several years will care more about the state of the motor than about whether there was a magnet attached or not.