I am currently running mine through the sun roof that I have completely closed. I tilted it open, ran the antenna, tilted it closed and haven't had any issues. Now, I am running the super thin coax that comes with Midland radio antennas that's included with the radio, so if you're using anything thicker you may get different results. I drive a 2003 Lexus GS300.
I am upgrading to an after market Midland mag mount and I'll post my results. I may wind up mounting it on the trunk and across the trunk weather strip, then through one of the trunk wall grommets through which all the other trunk wires run.
Kinda depends how much work you want to do. If I'm feeling really OCD I may just drill a hole through my trunk lid and mount a larger antenna.