Solid roof mounting is definitely the best way to go for any ham radio install. It gives you the best, most solid grounding.
Look for NMO mounts that require only a 3/8" hole - a bit easier to drill than a 3/4" hole. With that option, you do need to remove the entire headliner, which is a pain. All of the interior panels need to come out, then the headliner slides out of the back in one piece. There's a nice writeup someone did on this side about removing it when he installed a stereo system. The problem with having a sunroof is the limited availability of space. Reference the image I posted earlier - that's the closest forward I could mount the antenna and still leave room for the sunroof to slide back. I used thicker, low loss coax to feed that antenna since it's a 800MHz scanner antenna, but it wasn't hard to route it to the side and down the B pillar. If you have the time to do all of this, it's definitely worth it. It made a HUGE difference in the received signals.