"Warmth" is a product of the components used, and the specs used to wind a pickup.
The scatter winding of hand wound pickups
may produce a harmonically richer, more complex tone. That's a result of some of the frequency cancellation of the random winding pattern.
For instance, of the production single coils I've tried in my strats, between the APS's and the SSL's, which are wound to similar specs, the APS's are warmer, due to the AII magnets.
Of the handwound strat pickups, my strat Antiquities have a little more subtle complexity and harmonic richness. Due to the AII magnets, they are also warmer than, say, the Harmonic Design Vintage Plus set they replaced, which used A5 mags, and were wound to be a little hot. Those sounded a bit bright and brash to me.
remember that not all pickups are made to warm - some of vintage type strat recreatons are made to be bright, just like the originals.
That is my take on it - someone correct me if I'm wrong, though.
