I think I just found another "no scratch solution". I have a rubbery mesh that goes between the frame and mattress of my futon to prevent slipping when it's in the couch position. I cut a small square out and placed the magnetic antenna on that. It grips much better than the little rubber feet that came on the magnet, and there is no way it will scratch.
What have you guys done as far as going through the hatch? For now I'm just running it past the hatch seal, and unless there is an absolute torrential downpour, I don't think it should be a problem. I've been wrong about these things before, though. My other thought was to actually cut a slit in the seal, pass the wire through and then reseal with silicone. I'm not sure that's such a great idea, either.