Composer, I don't know as pitch recognition or playing perfectly in tune (if it were to be compared with some standard) is the "holy grail" of playing that some seem to think it is.  I have been told that intonation is not something that a violinist/fiddler ever masters, so much as being one of the elements of playing that one constantly works at improving.  Even for advanced players, from what I understand, it never becomes something they just take for granted in the sense of "mastering" it so that it takes no effort on their part. 

Of course, I can't say for certain if that is true or not, since I am relatively new on this instrument.  But it seemed plausible enough to me that I accepted it as a working premise and just went with exercises, practising and playing.  Over the months, if anything, I have gotten more sensitive to if a note I play is perhaps a bit sharper or flatter than I intended, and so it takes a consistent effort on my part to keep improving on that.  No teacher or method ever is really responsible for someone learning.  Learning is always accomplished only by the effort of the student and the desire to improve.  Books and teachers can't actually force a person to try.  That desire has to be internal. 

Ok, now about scales.. Personally, I class scales as exercises.  With exercises, think of calisthenics that might be done by soldiers or athletes as part of their training.  Such calisthenics are used to generally condition muscles and build endurance.  Usually the soldier or athlete won't actually be using the exact move of a pushup or situp when fighting or competing.  But it tones the muscles and helps build general consciousness of the body which can help with developing coordination as well.  A certain amount of such activity can be very helpful, but it won't teach the soldier how to fight, the athlete how to do their event, or the musician how to play.  Not by itself. 

I would tend to agree that the brain/mind prefers to memorize melodies.  I would put forth the further notion that it is much easier for the ear to hear if a melody or song is done "right" than for it to hear if a scale is correct.  It seems to me that it is better to go with the brain on this instead of against it.  Do scales and other exercises for the general muscles and condition of the hands and the endurance, but then work on melodies/pieces/songs for developing the ear and working on intonation. 

But to redirect to the original question, "how does an instructor teach you to play in tune?".  I personally don't know.  In fact, I don't actually believe that they can.  That sort of an improvement only happens when the student finds their own desire to make their playing sound better and puts in the work.  Teachers and books can give some possible suggestions, can encourage a regular routine that may be helpful in the long run.. But if the player doesn't want to sound better and work for that, then it isn't likely to happen.  The best teachers can find ways to inspire or motivate a student to work, maybe give them a methodology to use when tackling problems.. But the work is always something you have to do for yourself.

Just my personal view on teaching, really.  It's like in academic subjects.  The teacher can give you facts and make you have to regurgitate them on cue to pass quizzes.  But that doesn't teach anyone to *think*.  You only learn to think when you find the desire to do so and put forth the effort.

Kinda like the old joke..

"How many therapists does it take to change a lightbulb?"

"It only takes one, but the lightbulb has to actually want to change."