Most shakuhachi these days are crafted by professionals. These professionals spend years learning how to make shakuhachi, and they make every flute to the best of their ability. But, there is no getting around the fact that it is only possible for them to use their own bodies as a reference when making eachflute.
This comes into play for things like the shaping of the bamboo where it actually touches your chin, and in the placing of the holes (for longer flutes).
Everybody's chin is shaped differently. A shakuhachi can be very easy or difficult to play depending on whether or not the part of the bamboo that touches your chin"fits" your body well.
Sometimes a shakuhachi that doesn't fit you well can be reworked, making it immediately easier for you to play. (However, this is best done by someone with experience.)
With a choukan, or long flute, the positioning of the finger holes also needs to fit you. Often, the 1st hole is right of center and the 3rd hole left of center (when the flute is played with left hand on top), which makes it significantly easier to play.
Again,though, the positioning of the holes should ideally fit your body such that you do not need to struggle to close them.
(Some people insist that all the holes be directly on the center line. However, this has no effect whatsoever on the sound of the flute, and playing such a flute for long periods of time can lead to injuring your hands.)
Thus,ideally, you should have an instrument that fits your physique and physical habits. This will make it easier for you to play, allowing you to concentrate on expression rather than struggling with the flute itself.