Not sure why everyone thinks he's not with them. Just because they haven't said he is, doesn't mean he isn't. It would just cause more fuss if they said he was there.
It would be funny if JR did an iPhone video and was really casual about it, "Hey guys, what's up? Just wanted to show you around the studio, here's my eigenharp rig it's pretty good, this is my keyboard we've got some great songs around this Snarling Fucking Pig sound. Here's John Petrucci ('What's up guys?') and John Myung (...). You all know Paul Northfield hiding behind the computer there, and here's Rich Chycki who's mixing for us. Over here we've got Mr. Bosk, who is our new drummer (*smiles and waves*). Well that's pretty much it, it's really going great so far and we'll see all of you... on the road."