i think black pickups look better on the white/pearloid guard because that's how mustangs were done, and it's the classic look for that pickguard/electronics layout, which the jag-stang borrows while changing the colours.
i wanted a mustang when i bought my jag-stang... i 'settled' for it. so i always wanted to change the pickups to black covers for that reason, to make it look mustangish (i never did though).
i wanted a zebra humbucker with the black half closer to the bridge, then a black cover for the neck pickup. then you'd have the two mustang single-coil look with a discreet extra coil on that bridge pickup!