Oooo. Tough one. You are talking big, magnetic based one you are just slapping on the roof, correct?
Only clean way to do it, is to go from underneath, rather than the top. Look for a cab vent or drill a hole in the under foot plastic storage bucket and then caulk it all water tight. Unless you have miles of cable links, in the old days we would go through the firewall somewhere, but I sure hate to take a hole saw to a new truck, or start tearing out all the stuffing, insulation and pushing around all the factory wire harnesses for a spot to slide it through.
If it is just temporary, leave it as is. If you want it for life, you are going to have to get serious and drill, cut or tear into something.
*There are those "through glass" mounts that you could use on a flat rear window, but they only hold a small pigtail ant. and don't get much height to them like a good old whip.
