Layer visibility during batch rendering is supported, so if you set up a key frame animation using a third party plugin, you then have the ability to animate moving components. Batch rendering was not set up with this in mind, but if you can get the work flow figured out, I'm sure its possible.

Recognizing layer visibility in animation is on the list, and may be a possibility in the future, but that means re-parcing a scene for ever frame. That adds a lot of time with larger animated models.