the impression i got from him when i talked to him about amps when i met him after a show last year was that the Line 6 was really only for live stuff. Its a lot easier to carry around one modeling amp than a bunch of different tube amps and such. He said he liked it for the simplicity in getting a wide array of tones out of one machine.
I would imagine that he would use his tube amps (mostly Mesa Boogies as far as i know). They sound better, and im sure he would want the real thing for something thats being recorded