I have a portable unit in my 944 and I have the antennae "stuck" to one of the rear hatch shocks. I haven't had any reception issues at all. Not optimal, but if you're going to do a more permanent install, that at least may give you some ideas location wise. It should work fine through the glass. I also have another potable in my truck and it just sits on my dash.
The magnets on those things are usually pretty stong, so you might try a thin piece of plastic to eliminate or at least reduce the scratching potential.
I was concerned about that too on my cab, but the only real place to put it is on the trunk by the third brake light. This is a permanent installation, so it doesn't come and go like my other unit. The antennae doesn't move around at all as the magnet is very stong, but I do keep it clean and waxed to help reduce the fine scratches. If you search, I posted a pic on here before.
- Darryl