Option 1 replaces the glass, and by that I mean it does just that. The thickness of the carbon insert is approximately 0.160in thick, prior to clear coat, and therefore pretty closely matches the thickness of the glass. The physical size also matches the glass - or pretty close too, I'll include a sheet of sandpaper for any final trim sanding. The intent of this is to allow the installation to match that of the installation of the glass itself.
Because this option is simply replacing the glass and all other installation details are the same, I would anticipate it's going to be a bit of a PITA too. A person could probably get creative with different rubber gaskets to try and get it to seal up better, but at the end of the day the sunroof design does not lend itself to being completely watertight, hence the factory drains. I owe goderd a PM back and am going to recommend he check out TrimLok, http://www.trimlok.com
, for possible seals that might work for his desired installation method - goderd, I'm still thinking of a couple options and will get back to you this evening.
Hopefully this answers your question. If not, please let me know and I'll try to clarify.