D.K.
I think the pediatrician is worried about not having enough fat in his diet, which is why whole milk is recommended for the first two years. Breast milk is whole milk, so you are fine. The other things you listed that he eats also has fats, so again he is fine. Children under two need the fat for building blocks for their developing brain. Without enough fat their nerves can't grow properly. I know of an extreme case where the parents fed their twins very little fat because of their nutritional beliefs. At two years old they could not walk. Their nerves didn't have the building blocks they needed. Very sad.