That happened twice for me and once not at all. One of the times it happened, he was gone for several minutes. I think it has to do with how long it takes for the group before us to load. It's a way of keeping the pre-show going while groups in front load. The pre-show was timed a little differently all three times I did it.
That's just my guess. It didn't seem to have any particular reason. I thought it was strange, too, and it didn't seem to add anything to the story line. So my guess is that it is just for delay in loading purposes.