Given the two I lean slightly towards a solution where it is just a preview/export option. The issue here is the user might have used features that they don’t want for the target output style since everything is available. But perhaps the option could be clear like “Export Limited Current Scene and Main Timeline as CSS3” so that there’s some ahead-of-time indication. And then if there are other features like timeline actions used it could warn at export a la the browser support.
I’m not a fan of lots of choices when opening the document. Flash had this, and I always felt like I’d be boxed in by my choices. Further, it would seem “CSS3” might be the standard choice, so users could be using a very limited version of Hype without really knowing there’s so much more!
Those are just my “developer notebook” thoughts - sometimes things need to stir around a bit or new features come out that help bridge the issues.