Motability are usually pretty reasonable. If they ask about fitting a tracker, just tell them the truth as you’ve put here – explain that it would terrify your son, render the car completely useless for his purposes (which is what the whole point of the scheme is) and that you would rather be without the car than have to deal with the consequences of the tracker being there. I personally wouldn’t call them in advance about it – I’ll be honest, the first thing I would think if someone was trying to avoid a tracker would be that it probably means a tracker is justified, but that may well just be the way my mind works.
"Man is born in freedom, but he soon becomes a slave, in cages of convention, from the cradle, to the grave."