I just watched it - incredible animation, thanks for posting the link. But I don't know what you mean about the eyes. I watched the animated clips at the end a second time. To me, they look like the same eyes we see on the puppets when we see them in the workshop.
The pig in this movie actually got real eyes of a teen tracked in. That looked awesome. I can't find a link for the full movie and the trailer here doesn't give more than a few frames near the end. But it's a really effective way to give life to a lump of silicone. I was only involved in the casting of the puppets, but I saw the CGI work of Lasse Smith.