hmmm... good question. I haven't been through that article in a while, but my guess is a few reasons:
1. Obviously to showcase the flash communication server.
2. The comm. server allows a bit tighter control over the video quality/bandwidth usage. It also let them create one swf, while still providing a high-bandwidth stream as well as a low-bandwidth version.
3. Firewall testing! Macromedia is currently working pretty hard to get the comm. server working through most corporate firewalls, and this gives them a chance to do some testing I'm sure.
But, you are right. It could very well have been done without the comserver. One nice thing with netStreams however, is that you can also record "data" into the stream. I'm guessing this is how they synced the animation to the video.