When people have "leaky gut".... things pass into the body that shouldn't. This stimulates the immune system, and part of that involves inflammatory cytokines... including histamine.
It is this cascade of inflammation/histamine that causes the grief.

Also some peptides, being protein in nature can cause antibodies to be formed, and these can then attack parts of the body with protein sequences that are similar. Some reactions are confined to the joints, some skin, and some nerves, etc.

Many patients with autism for example cannot tolerate casein that is the peptide in dairy. So many autism treatments involve gluten free/casein free diets. Casein is thought to involve the central nervous system mostly.

Many are allergic to soy and some even corn. My son's friend from high school went deaf from corn. When that was uncovered in allergy testing, she went corn free and regained about 25% hearing, and now uses hearing aids. In her case the corn gluten, attacked the auditory nerves.

Everyone is different... genetics I guess determine what system will get attacked when allergies and intolerances exist.