As per Sheldon's article, it looks like paper EDH (now to be called Commander) and Online Commander (to differentiate it from paper Commander) will be syncing up rules wise. Here is the relevant link:
One of the most important spoilers is this:
"One of the side meetings I had was with Aaron Forsythe, Scott Larabee, and Dave Guskin about syncing up the online and paper games and rules. I'm happy to report that barring programming concerns—some of these things just take time—the online game is going to end up as close to the paper game as possible. Dave had done a great job of finding all the differences, and then we went down them one by one, agreed on solutions, and prioritized them. Hopefully you'll see the fixes in the near future, the most significant of which for now (IMO) is the removal of the Superlegendary rule for Commanders online."
This is a big change for online, and multiple copies of the same Commander in play at the same time will now kill each other, AND Clone/Copy effects will ALSO kill Commanders.