There's an online allergy recipe site that might be helpful for both her and you:
http://www.foodallergykitchen.com/
Something she may not have even thought of, is that a "milk allergy" is more properly a "cow milk allergy". Her little guy may be able to have goat milk and goat milk products like goatmilk yogurt.
Also, there are soy-based protein supplement powders on the market (I've no idea about brands or anything, not something I've ever used), which could be mixed into soy shakes or banana muffins etc. Of course, since I've never used them I haven't read the labels, and they might have casein or other milk product derivatives. THAT is the problem with milk allergy. The byproducts are in practically everything. Things people wouldn't even suspect. (Corn, wheat and soy are like that too.) It's really stressful and upsetting to try to find any convenient food when you're dealing with that.
Avocados are calorie dense and have fat, he might like mashed or sliced avocado.
The thing that worries me is that he's falling behind on his growth chart. It doesn't sound like he grew a bit, hit a plateau, grew some more, and so on. And that her doctor hasn't ever shown her one is so odd! I thought they ALL did that these days! I am usually pretty protective of not alarming moms with small kids (I have a shrimpy little fellow myself), but this would worry me too. I don't think you're being over-protective.
At least have the chat with her, and just let her know you don't want to upset her, but you love her little boy too and want to be on board with them in helping him eat a well-rounded diet. And that maybe if he's "picky" (like all 2 year olds, hah), that a safe food for him that he wouldn't try at home he might eat for you.
I would talk to her about this before doing anything with his food, though. His diet does seem out of balance, and low in necessary fat and protein. Dealing with food/allergy/oral sensory issues is challenging and stressful.