Not a single one of these factors will change the tone significantly. But when all added together, the sum of the parts is better on older vintage Fender pickups. Also vintage Fender magnets are Alnico and not Ceramic. Finally, as time goes on older magnets lose some of their power. The less power the magnets have, the better the strings can vibrate.
Powerful magnets can actually pull the strings towards the pickup, dampering the vibrations.
So there needs to be a balance, because you don't want too strong or too weak magnets. That is, the height of the individual magnet pole pieces. But prior to Hendrix, most players did. To compensate for this, the fixed magnet heights were different on older Fender pickups. The handwinding tonal difference may be due to a lack of distributed capacitance when scatter-wound.