can you explain diff b/w MSPI and allergy

At 11 weeks old my breastfed daughter began having unexplained nasal congestion and was fussing at every feeding and her stools were green and foamy. By 12 weeks she was refusing to breastfeed altogether and I was giving her expressed milk in a bottle. After several trips to the pedi and an upper GI, they finally diagnosed her with milk/soy allergy. The upper GI revealed damage to her duodenum so they put her on 15mg prevacid solutab. I immediately started the elimination diet and have been on it for almost a month. She is getting better and is back on the breast with the occasional bottle in the evening when she doesn’t want to eat. Her poops are less green, but they vary from day to day. Yesterday was more yellow and typical BF poop, but today it was more green and a little slimy.

My question is–based on her symptoms and the results of cutting out dairy/soy and basically everything else does she have a protein allergy or intolerance? What is the real difference when dealing with a breastfed infant?

I’m asking my question here because everyone seems so knowledgeable about these conditions and now I know why. The medical community is also confused and you can’t get the same answer from two diff docs. The pedi GI said to just stop BFing and put her on Nutramigen. I don’t see why I should do that if she’s getting better.

Thanks so much for reading and I hope you can help us understand what we are dealing with.

I should add she’s never had blood in her stool and she’s never had a rash.