Don't be afraid to drill through the roof if you need to. Sometimes that's the simplest, most direct approach. Dicor is your friend in times such as this. Here's what I did two years ago. No leaks at all.
Drat! no photos. I hate the way this site handles photos.
I cut a nice round hole with a hole saw, inserted a length of 3/4" pvc conduit down into the rig inside of a cabinet. Cut a 3/4" hole in the bottom of a non-metallic junction box and slipped it over the end of the conduit, dicored the snot out of the edges of the box an pressed firmly onto the roof surface. Viola! You can now route your antenna cable into the junction box and distribute it where it needs to go.