There's a lot of errors on Vitali's part. For example, he ends up describing the aspect ratio situation wrong... he's confusing the video transfers with Kubrick preferring not to shoot in anamorphic formats like Panavision. Kubrick's widow mentioned in an interview that Kubrick actually wanted to participate in supplemental material after he retired (after Eyes Wide Shut), but it never happened obviously. I'm fairly sure that she hinted at Kubrick being interested in recording commentaries.

As for the Dr. Strangelove alternate ending, I'm fairly sure it's just lost. Columbia also lost the original negative. It only survives because Kubrick kept a pristine fine-grain positive in his personal collection (well, other than some grainy and dupey 4th generation prints in Columbia's collection). Columbia used to take horrible care of their films. The negative for Lawrence of Arabia was being stored in a 80 degree abandoned bowling alley at the time it was to be restored (back in 1988). From what I've heard, until their restoration program was started in the late 1980s, it's a miracle that so much of their library still survives.

Kubrick was quite the packrat, so the deleted Shining stuff is probably all there somewhere (either in his archive or at Warner Brothers). I mean, Charlie Chaplin insisted that hundreds of cans of outtakes from his films to be destroyed, yet they still exist.