Commander is EDH. The format that was called EDH is now called Commander. As such, Emrakul is banned in it. What ramifications this has for the online version of the format, I couldn't tell you, but I would assume that any differences will be erased, and that they simply haven't gotten around to doing so yet.
however, if you want to play Wizard's version of EDH, by all means. We've banned Emrakul pretty much before he was banned because we actually like to have fun in our games. He sucked all the fun out of it.