Thanks! Your question is hard to answer. I've played MIM and American made strats (and a classic vibe squier or two) that I liked just as much as any guitar I've ever played.

I will say it's easier to find a great custom shop guitar than it is to find a MIM or American. I've enjoyed every C.S. guitar I've ever tried out while there have been plenty of MIM and even American guitars that were complete duds.

But, for me, the really special thing about Custom Shop guitars is how different each individual guitar is from every other. When the contours and the curves and the necks are all shaped by hand, you get huge differences in weight, sound and general personality from one guitar to another. I've played quite a few Custom Shop '60 strats, and they've differed in weight by as much as a pound! That's not something you find as much in many production line strats.

Sorry to kind of dance around your question, but saying Custom Shop guitars are better is very opinionated. A great guitar can come from anywhere and anyone, your chances of finding one just improve when you include custom shop guitars in your search.