Lizzie I don't know the answer, but I am guessing if a dairy intolerant baby is receiving the milk protein through the breastmilk but not gaining weight well, and the poor gain is DUE to the dairy intolerance and not anything like genetics then:
that baby would need to have quite a severe intolerance, be in alot of pain, and probably fussing on the breast, and not feeding too well, and thus FTT.
Hand in hand with the severe intolerance would come both due to pain and inflammation of the digestive tract. I don't know how serious the intolerance needs to be so that nutrients are not being absorbed well and thus affecting weight gain, but I suspect quite bad.
I say this because of my experience with DS1 who had MPI and he was absolutely huge and thirving, he was in pain for the first 4 months of his life with undiagnosed dairy intolerance and reflux but he just fed really well and grew and grew. He was in 90th percentile until he was 1 years old. At 4 months old I cut out dairy and it didn't affect his weight gain at all. His MPI was not severe, I was able to eat hidden soy and hidden dairy, and it didn't affect him. He was eating dairy by 9 months old when he outgrew his reflux.
Now a different story, here I have my DS2 smaller, and gaining weight a little too slowly, whist I am on an ED eating no allergic foods at all and very little intolerant foods, with very little fats but still a diet high in nutrients. He feeds really well, I have plenty of milk. The weight gain has slowed in the last 3 weeks - since i have been on this diet.