Assuming the article is completely accurate, the doctor's phrasing and mannerisms (e.g., shaking his head, emphasizing not only that the child is in the bottom 1% but that 99% are better than him, "seemingly perplexed"), don't seem consistent with your explanation. His comments and tone don't strike me at all as being encouraging or reassuring, he just sounds completely dumbfounded by the parents' situation, almost as if he pities them for having such awful lives.
I didn't read it that way at all, either. It was sympathy and amazement. Shacking his head in astonishment, and perplexed at how they can handle what they must.
Maybe it's because I've been on the other side, seeing that shaking head and being asked that question, but it doesn't at all come across anything less than support and encouragement.
