You could also put a thin material as buffer between the magnet and your car.
Depending on how strong the magnet is, you could:
Put a really thin fabric under the magnet like one of the soft fleece things people put into their laundry to perfume it or stop colors from bleeding
A tissue paper might do as well. You can change it regularily to avoid dust scratching your paint
Tape the underside with masking tape. The slightly crincled texture is flexible enough to avoid scratches
All these materials have to be changed regularily to dispose of dust particles that would otherwise scratch the paint. Especially if you drive on construction sites you want to change the buffer every time.
An alternative offered by Ellesedil is to apply the buffer to your car permanently:
There are actually automotive products on the market that are essentially a thin material, specifically a transparent film, that is applied to the car with the sole purpose of protecting the paint. The shorthand term for this film in automotive circles is "clear bra" and is designed to be essentially imperceptible unless viewed up close. This provides really long term paint protection and removes all of the drawbacks you list in your suggestions. But, it costs a little more than a box of tissue paper. Other options also exist, but a clear bra best matches what you suggest in your answer. – Ellesedil