1. TAP Plastics is the local source, probably the cheapest as well since you don't have to pay shipping. Oh, and they have the rarest feature of stores up in the city....a parking lot! I'd get whatever their thinnest material is if you just want it for cosmetics.
2. My large tank has some sort of plastic bottom, I'd guess PE, but could be anything. I don't think it's acrylic. It's about the color of sand, which I rather like. I mention this because I know clear is a different price than black, so tan might be different again. If you just want a reef safe plastic, many are fine, although some will stick to silicone better or worse than others.
3. I'd go with a matte finish if it's an option. It's not going to stay shiny for long and the scratches will stand out less.
4. If all goes well, plan for it to be covered in coraline at some point.
5. My current tank is bare bottom, although only because I don't plan for it to be permanent (next one will have sand, I already have the sand even). I just blow a powerhead under the rocks periodically and blow everything out. It's definitely easier than sand where you can siphon exposed sand, but not the rest of it. As to which makes a better reef I don't know.
6. My vote is to just make it fit well to the bottom (this will require clearance for the silicone), let the weight of the rocks hold it down, and ignore the small gap underneath. Sealing the edges with black silicone also seems like a decent option.