Contrary to what I said earlier you can export transparency for 4.0.2. The only thing is you can't export it after you've rendered. If you render it exports the render file. If you don't render, the preview window in QuickTime Conversion says unrendered and that's what you think you're going to get, but if you export you do get transparency. I tried it in Animation and PNG. They both worked except PNG took more than twice as long to do the export.
All the best,
Tom