I'll do the Jeopardy thing:

A: Take the antennas off the roof during a rain storm.
Q: How do you prevent water from entering through the weather stripping with
a mag mount antenna during a rain storm?

So let's say I'm looking for another alternative. I am using mag mounts
because I don't want to permanently modify the car, but I would like them to
be permanent, in that I don't want to remove them until I sell the car.
Right now I am bringing two coax feeds in through a rear door, but it leaks.
I am going to try the hatch door and sunroof, but failing that, is there
anything I can do to keep the water out?

Thanks