Exporting Multi Layer Quick time files?

You can of course manipulate the transparency as you want and turn it into an Alpha channel. The problem is just that it will always affect the RGB info. You cannot have an inert Alpha and a completely different RGB. AE simply doesn't know how to do this unlike e.g. Nuke where you can create any custom channel you want.

Mylenium 

I don't know of any video codec that supports layers. 

My workflow is to export a LOG file that matches the LOG file in the Editing app, or export a Log file of just the effects with transparency where the background or foreground elements are, then stack up the layers in Davinci, or Nuke, or even Premiere Pro so I can do the final color grading there. 

If you really need layered files, then Open EXR image sequences are the way to go, but you can't really really get a beauty pass, the original, and some masks in the same way that rendering separate passes of the comp with effects and masks turned off and on would give you.

This is not possible. I'm not even sure if this would even be useful. Performance for decoding such files would be terrible and you don't get anything you couldn't do with image sequences.

Mylenium