My take on this. I have no references (except personal experiences) so you might downvote this.
I assume that all western wind instruments has a history going back to "simpler" instruments without keys. The oboe has roots back to the Shawn, the clarinet has roots in the Chalumeau. Each has been "improved" over time with differing placement of holes and adding keys. Some of the other examples, like the saxophone are much later inventions.
If you look at these instruments, they use three fingers in top hand for major scales (all instruments today are played with left hand at top, historically some instruments could easily be played with right hand at top, example is the bassoon forerunner dulcian). Why you might ask? If you look at the tin whistle, the most "basic" instrument, it sort of becomes appearent - simple ergonomics. There is no good place for a hole for the left pinky. The smallest finger is also the shortest and in order to reach a hole for that you need to displace the hole towards one side. Easier to only use three fingers for the left hand. The right hand similarily uses only three fingers on the tin whistle, the fourth finger is sort of an added extension on many instruments (the dulcian has a key for bottom hand pinky that can be played either by left or right hand).
So now for the selection of intervals between fingers. The instrument should be able to play a western scale in order to be usable. This requires 7 major tones and as many as possible of the others up to 12 tones. The reasons for this goes back to at least Greeks well before start of our time reckoning. Using 6 fingers you can have all of the 7 major tones (6,5,4,3,2,1,0 fingers). The question remaining is how to divide the intervals between the fingers, half-tone intervals or hole-tone intervals. Again, a bit of ergonomics come inte play. A full tone interval is sort of easier, further away, than a half tone interval. So the ergonomical choice is hole tone intervals between the fingers in each hand. This leaves a bit of leeway for the change between hands - where to put the half tone interval.
There are variations on how to place tone holes on older instruments as well. Some examples include: the ocarina, the rackett bassoon.
So in order to answer your question: in my mind it is a combination of western tone scale having seven major tones using only six fingers, and the ergonomics of placing the holes in order to make a playable instrument.