The dude in the chamber can't be Bill Vaughn. When Bill Vaughn was killed, the could only identify him by his dental records.
Syd could only be identified by her dental records too and we all know how that one turned out!
I've said it before in another thread and I'll say it again here, the guy in the chamber is without a doubt, Rambaldi, but who is Rambaldi? Bill Vaughn. It makes sense with the prophecy, through the chosen one will come Rambaldi's greatest works, Michael Vaughn is son, Syd's having his baby, it all makes sense. Not to mention that if Rambaldi is still alive, that gives us hope for Vaughn.