There is no way hand manufacturing is going to meet the quality & consistency of well engineered & computer controlled, CNC & threading machines. Your going to start seeing pickups of very high quality mass produced & affordable product all over the place soon. Of course there will be some that still swear by the work of the Jedi but it will be a dying religion in the near future.
CNC machines are just tools used in the process of building a guitar. It is often described as if it's a magic guitar making device. But, CNC made guitars are not automatically better or worse. Some of them end up as fantastic guitars, some average, and some turds. The difference often comes at the end of the process when the guitars are finished by hand.
Many great budget and boutique guitars are made without the use of CNC. Rondo Music guitars come out of Korea made with old fashioned tools and methods. Some of them end up as pretty great players according to folks around this forum.
By the way, hand wound pickups are not completely wound by hand. They are wound on some type of machine. But, an uneven and imperfect wind, tends to result in more complex tone. This is where your CNC theory on computer perfection in creating a better sounding pickup fails.