I don’t know about the scratching, but I wanted to mention that it seems normal for many rabbits to have “thinner” fur just behind the ears in the nape of the neck area. I don’t know why that is, but if the spot is not truly bald, just less dense/less amount of fur, I would not worry. Rabbits seem to focus on their head area a lot when grooming, and pulling the ears down is part of that, if the vet checked him out and found no mites or other problems I would not be concerned.
Of course he could be overgrooming, but I’m not really sure what to suggest if that is the case and it is behavioral/stress related. I just wanted to point out that’s it’s normal for the fur to be different just behind the ears. You may also see thinning of the fur if the rabbit is going into a molt, and that does sometimes start on the face (though I read usually on the forehead for rabbits that molt face first). “Bald patches” are not always a sign of a problem, but you did the right thing to take him to the vet.