MK uses Fralins in the Suhr guitars. The only other pickups I ever heard Mark to put into his Strats are Seymour Duncans.
I can check with Seymour if perhaps he did some other PUs for Mark as well...
With regards to not understanding why Mark chose Texas Specials. There are a couple of reasons.
1. Marketing: in order for Knopfler to receive a signature Strat, it was supposed to be spec wise different from the standard Fender range. The standard range at that time was the American Vintage (AVRi)1962 Stratocaster with a 7.25 board, small frets, 57/62 pickups, rosewood slab fretboard. This standard range is (on high level) spec wise the same as the pre-CBS 1961 Stratocaster MK played at Dire Straits. So what was Fender supposed to do? Take the AVRi, make it hot rod red? That would not suffice the need for it to be different and launch as a Sig Model. My guess is that Fender proposed Knopfler something that would allow it to be different and sexy, so they went with an ash body (marketing story: it was as light as pre-CBS alder), they put on bigger frets to advertise better playability, they added the pickups and they made the exclusive color. Now THIS was enough to justify a signature model.
2. The ash / rosewood combination of this Strat is not usual. I have written above - this combination makes for a very BRIGHT tone. The Texas Specials offset this with their midrange honk. Installing other PUs is always possible, but you run into risk of getting a very bright tone. Decking the trem will help but not completely eliminate this. Ash normally works better with a maple fingerboard which has less presence (sounds "rounder").
