With the "persistent top-level content" feature introduced a few weeks ago, all the content in the top-level collection is now downloaded and will not be removed from cache. That way, users have access to all the top-level content as well as other cached or explicitly downloaded content when they're offline. I assume that when you opened the Natural History Museum app, the top-level content was being downloaded.
Regarding the "Update Available" prompt, which some people call the "update pill," I'm not sure if there are plans to allow automatic updates.