I don’t see a reason for stashing the Epub inside the Kindle file other than because they are planning ahead for a switchover. Actually, it would be more accurate to say they are giving themselves the option of a switchover.
FYI: KindleGen is a command line tool for making Kindle ebooks. If you’re using MobiCreator or MobiGen then you will probably want to use this instead. KindleGen supports larger image sizes as well as the video and audio tags for embedded content (for ebooks like Nixonland).