Because the size and the position of the holes create a scale which can be used for playing music. Via links shown in an earlier comment it's explained that it is a diatonic scale, but the point is really that if the holes had different sizes and the positions were different, even slightly, then you couldn't play music as we know it (see the video where Albinoni’s Adagio is played on a replica flute).
That's why it can be stated that it wasn't accidental.
"the size and the position of the holes cannot be accidental – they were made with the intention of musical expression."
Cannot? Were? I'm sorry, but there's no way to actually deduce that from the available information.