Whoops -- I think you're missing a big part of the point of compiling into "standard" JavaScript. Not only is CoffeeScript code fully compatible with any JS library ... it's also compatible with code generated by any version of the compiler, and with code generated by alterna-compilers like Coco, and eventually this project as well. The semantic compatibility exists at the "plain 'ol" JS level.
That only solves part of the problem. It's still a big pain to have different syntax dialects and different tools that have to be used for different projects that are ostensibly written with the same language, even if they are compatible after you compile them to JS.