I see what you're talking about. You'll also see it on the launch page when you first click the link on the iPad. That's the auto-generated thumbnail.
You can select the starting thumbnail from the Publish > Project Info window:
In my case, I only have one slide and the slide includes the hotspots. I could see where we would want to exclude invisible items from the thumbnail so I'll send that in as a feature request.
You can swap out the auto-generated thumbnail using one of your own by going into the published output and updating the thumbnail.jpg file: