Yeah, they use more distortion live - but they still do it in moderation. When I saw them, they ran the GT-6 pedals into Marshall JCM800s. So the distortion was up there.
Of course it's true that the guitar, pickups, amp and whatever else factor into it. I mean the PRS is an amazingly versatile guitar, and with the Full Shred and Jazz, they can get all kinds of tone.