He voices his amps to work with any guitar and pickups. Thats what the eq and other controls on the amp are for. If one guitar is too bright, you can eq the brightness out, and vice versa. If one has hot pickups, you can turn down the gain. Just like any other amp.
However, in an effort to try to answer the OP's question, there was a comment left below the "2008 CCV Namm" clip (on YT) that shows Mark demoing the head:
"The guitar is a homemade one that Mark put together himself. PUPs are DiMarzio Super Distortion (Bridge) and ESP rails neck (pulled from old guitar). Very Nuno'ish though..."
I have no idea if this guy knows for sure, but he spoke of it like he knew Mark. I know Nick knows Mark very well, so maybe back in 08' he used a different type of pickup than he does today...... And again, it could just be a description of the guitar that Mark chose to take with him that day to the NAMM show.