"Our entire systems of "western music scales" is based (partly by accident) on each tone in a chord being "in step" with harmonics of another tone of the scale. Once the learner has developed the ability to "feel" being in tune singing the same note as another singer, the same ability to find the "easiest tone production" in synch with a harmonic of another voice should be fairly easily developed with a reasonable amount of practice."

Possibly the problem lies at least partly in the use of equal-temperament instruments in school music lessons. The child sings a natural interval, but the teacher hears the note as being out of tune because it's not the ET equivalent, and condemns the child as "tone-deaf", when in fact it's the teacher's ear which has been trained out of natural scales, which non-keyboard instruments still use. Just a thought.