I have no idea what the theory is behind it or if it really works, but I have heard of it before. My mom had to do this for my younger sister because she was having similar issues with whole milk. She ended up on boiled 2%, but this was back in the 1970s so maybe your doc is just old school. I wonder if the boiling does something to break down milk fats or proteins.
ETA: I found this 'If the milk is pasteurised, boiling it will assist in the digestion. Pasteurisation partially dismantles the protein structure. This makes the milk more difficult to digest. Boiling the milk finishes the process and decreases the chance of allergic reaction (1).' from this naturalparenting website.