I do think you're correct to assume that he will choose the foods he needs if you offer him a wide variety of natural foods. There was actually a fascinating study done in the 1930's where babies in an orphanage were offered 33 different whole foods at every meal. The foods offered included cereals, meats (including organ meats), seafoods, bone marrow, eggs, milk, vegetables, fruits, and salt. Nothing was sweetened. The nurses who fed them were instructed to sit quietly with a spoon ready and to make no indication or hint of any sort to the babies as to which foods they should eat or how much. They were only to help feed a baby when the baby clearly indicated which food he/she wanted. Everything was recorded: the amounts of different foods eaten and spilled, bowel movements, height and weight. The babies were regularly x-rayed to check their bones and given blood tests to monitor their overall health. Though their diets were each quite different and sometimes appeared very limited in their choices, they were found to choose relatively similar amounts of macronutrients when each diet was looked at as a whole. Each child also seemingly chose specific foods that contained the nutrients they needed. For example, one baby with rickets ate cod liver oil (high in vitamin D) every day until the rickets was cured. If you had looked at their food choices for one day or a few days, it might have appeared unbalanced, but overall these children chose a very balanced and nutritious diet.
So yes, it's important to let babies follow their cravings to some degree because there is wisdom there, at least as long as the foods offered are unprocessed and healthy. On the other hand, if you're dealing with a child who has had commercially-processed foods before (which is practically every kid, right?), a lot of those foods have addictive qualities. They just kind of throw off your whole innate "compass", so-to-speak, that guides you to choose foods that have the nutrients you need. Many are hyper-palatable to a degree that natural and minimally processed foods can't match, and there's a lot of recent research that indicates that the obesity crisis has a lot to do with the excessive palatability of modern foods.
I generally let my son (3 going on 4) choose what he eats as long as it doesn't inconvenience me excessively, and my only rule is that he has to eat a decent amount of something containing protein before he is allowed to have treats (which are generally healthy treats anyway). The protein thing is largely for my own sanity because he gets extremely cranky anytime he eats a meal that is very low in protein (actually I think pretty much everyone is this way, we need complete protein consistently throughout the day to make neurotransmitters in the brain so we feel normal and happy). It's worked out really well for us so far, and I think his diet is really pretty good overall, despite him basically choosing what he eats.
That's great that your baby eats so much ghee. It's a great food for babies. You are so right about fat and babies brains! We usually do butter in our house, but when my son was a baby one of his favorite foods was an Indian tomato chicken curry that I always made with a ton of ghee. He could not get enough of that stuff!