I have some ideas about your thoughts, because I have had the same thoughts.
My son has a spot that looked like a cavity forming. It has been checked out multiple times, and it isn't a cavity. I have seen on this forum before a mention of butter oil being helpful to re-mineralize the teeth, but if the kiddos are intolerant to dairy, that doesn't help much. I think getting more mineral rich foods would be helpful.
I was frustrated about my son having food in tolerances and getting sick too. One thing I recently learned in a class I am taking for a nutrition consultant program is that GMO foods have the possibility of causing more food allergies. Any soy, corn, or wheat has the possibility of being GMO regardless of whether they are organic.
In an ideal world, our children wouldn't get very sick, very often. However they are exposed to environmental toxins constantly which are beyond our control. I am sure this causes some allergies and illnesses. I notice my son does get sick fairly often this winter after going to Preschool, but he gets over the illness quickly compared to other children I know. I think eating the way we do helps our children to detox much better than the average child who is eating HFCS, sugar laden foods, injected toxins and toxins from so many foods and other daily things like toothpaste, soap and so on.
One way that I have found TF to be beneficial is that my body rejects junk food now. If I deviate too much from my healthy diet I feel awful or get sick. So I think there is some benefit, it is just hard to see it clearly. There is so much healing to be done from all the previous years of SAD dieting. It is bound to affect our children. Getting sick exercises the immune system to our benefit as a children if we let the immune system work to do its job natually and not give a bunch of medications and antibitocs. I think getting certain illnesses as a child theoretically decreases allergies and intolerance as they get older and also creates a stronger healthier immune system as they get older too.