Thanks for the suggestions, however the hole drilling was DOA (my bad as I should have specified it was a non-starter). On my 1990 Miata I have a tuned splitter that allows me to use the stainless steel antenna mast, but that isn't an option as the Jetta has a shark fin antenna. None of the hatch clamp type will work due to the lack of clearance between them and the body (if there was room I'd use that type of mount as it is what came standard on my K40).
Well, doesn't leave you a whole lot of options. You are going to need to get creative.
I've got a friend that wanted to run an HF rig in a Mini Cooper. He removed the shark fin AM/FM/Satellite antenna and fabricated at mount that would allow a screwdriver antenna to be placed in the hole. Looked goofy as hell, sort of like a bumper car with the tall antenna sticking up, but it worked well.
Glass mount antennas don't work worth crap, unless you only need a very short range.
Usually when I get in that sort of situation, I take a trip to the hardware store and just wander the isles until I get an idea. Usually you can find a bracket or mount that will do something.
As for possible leaks caused by the coax entering via the hatch opening, I always route wires and cables so a drip loop is created BELOW the lowest opening of the hatch/trunk - never a leak in over 40 years!
Yeah, that's a good plan.
However, water intrusion into the inside of the car isn't the only issue. Depending on how you have it routed, the coaxial cable can get pinched, which changes it's characteristic impedance. Probably not enough to make a difference to a CB radio, but something to consider. Pinch it enough, and you can damage the cable enough to get a short between the center conductor and shield. Damage the jacket, and water can get into the cable and corrode the copper.
But careful inspection and routing can address that. Whatever works best for you is the right choice.
Let us know what you figure out. It's going to be a challenge, but not impossible.