So if I understand correctly (and I'm not sure I do) they originally had him eating low-carb snacks and foods that made it easier to care for himself (due to having established carb counts) and they moved him onto snacks with carbs and food that is more complicated for him/his parents to carb count? I understand wanting to get him off prepared food, and that's definitely good overall, and it is cheaper which is the goal of the program, but it sounds like they might not have taken into account what the kid and his family's goals and needs really were.
As to your original question Dr D., it's as what Patti says. Nutrition recommendations have had things by the wrong end of the stick for a while. Fats, including saturated fats, are not bad for you and in fact can be quite good for you, same for salt it's now coming to light. A lot of health problems, on the other hand, can be linked to a high-carb diet (or a low-fat diet which typically replaces fat calories with carb calories). If you don't give your body good quality ingredients to work with (for example in the case of cholesterol) it will put out shoddy stock and that's where the real problems start. Add increased glycation onto that (high carb content in the diet means more sugar in the blood blood means sugar molecules getting "stuck" on lots of different tissues - joint tissue, arteries, cholesterol molecules, etc. - and gumming up the works) and you're really in trouble. The best thing is to eat plenty of non-starchy vegetables and good quality proteins and fats, including meats, fish, eggs, cheese, nuts, use moderation on fruits and keep to a minimum on starches (including bread, pasta, rice, cereal, potatoes, corn, etc.) and sweets. And to eat a big variety of foods so you're sure to get a good balance of nutrients!