He sure did it awful quickly, the site also credited "- Silk Road Staff" at the bottom of the message. Then there's downtime messages from time to time, it seems rather unlikely that MK is DPR but there very well might be something behind this. The domain wasn't registered to John Smith, it was registered in the name of a company that Mark Karpeles owns and pointing to Mark Karpeles name servers.
But their argument is that Ulbricht founded Silk Road of his own accord, then handed it to the "real DPR" months later. (Only to have it handed back to him just in time to be arrested!)
That's really bad reasoning on the part of the investigators. Registering a .org domain name similar to the name of your secret underground site is a stupid and completely pointless thing to do.
Both Ulbricht and Karpales are known for doing stupid and pointless things, though (hiring fake hitmen with hilarious emails, and writing ssh servers in php, respectively).