At the recent conference, I had a chance to briefly discuss this with Drexler. They'e aware of the problems with the current version of the animation, and intend to address many of them in the new version. As well, I had a chance to talk to a certain heckler, (Attendees will know who I speak of.) and your concerns are valid with respect to him. But I think most people will be able to understand the difference between a concept, and a completed design.

A better link is http://www.foresight.org/animation_challenge/ which has some discussion of the challenge plus links to the slide show and animation.

While the film will probably succeed in giving people a better idea of how a nanofactory could work, it may also be open to nitpicking from critics as various details are challenged. It's possible that the film may hurt the nanotech cause by in effect forcing defenders to commit prematurely to a possibly flawed design.