I think that creating 3D content using a WebGL-based application and then allowing export to 3D CSS may be a better solution rather than just creating the 3D in a CSS special purpose application. But admittedly, I'm biased because I'm a developer behind http://clara.io
You're right, 3D CSS still has a usecase though, it's just very restricted. Clara.io looks like a pretty sweet tool btw!
Clara.io is built using ThreeJS as your article recommends. I'm actually the third largest contributor to ThreeJS by commmits, so we are giving back where it matters too.