Mark Knopfler still does use his traditional strats (alder or ash)... that said, the MK1 that pensa made for him was designed to essentially function as a combination strat and Les Paul in one... to what ever degree one can achieve that. His pure strat tones (on the new album/What it Is/Sultans) are strats... his growly tones are a 59 Gibson Les Paul... and of course there are a variety of other guitars too.
Pickups are texas specials for single coils, and a vintage '59 PAF in the Les Pauls.
The white pickups on the original MK guitar are EMG (humbcuker pickup/sa single coils), but the EMGs are active pickups, powered by a 9V battery. They sound great for some things, and are a great way to recreate studio recordings pristinely in live environment. I preferred more organic sounds.
The Fralin Vintage Hot single coils are really a great combo with the mahogany body, which tends warm. The growl I get our of the Duncan Alnico II trembucker is sweet... I still would like to hear a Seth Lover.
I really dig Knopfler's tone, and my new guitar has done exactly what I wanted it to do... it allows me to go back and forth between his different sounds using the same instrument.