I don't know what kind of single coil Murray had in the original, but I'm quite sure he never had it connected, that way he could he get like a killswitch effect. It's possible that it was the stock pickup still in place.
The single coil pickup in the production model was a "Vintage-style Strat Single-Coil"
http://www.musiciansfriend.com/guitars/fender-dave-murray-stratocaster-electric-guitar#productDetail
Fender used it on their 50's reissues as well.
He went back to the Dimarzio Super distortion and PAF with one of his new custop shop Fenders in 2016, after using the signature model in 2009 and 2010 for a few songs in the set.