In short there are no differences between the digital download version of StarCraft II and the one in the boxed version, with the Blizzard rep saying, "All the files are exactly the same, but you obviously don't get the box, DVD, or manual." Also, If you get a boxed copy of the game and add the included key into your Battle.net account, "the option to download the client online will become available." The game client is region-specific, however. As the Blizzard rep explains, "Therefore, in order for a player to log in and begin playing, both the StarCraft II: Wings of Liberty game license and the installed game client must be from the same region. If the game license and the game client don't match, the player will be unable to login."
Gallery: StarCraft 2 Screenshots