There is a world of difference between an allergy and an intolerance. An allergy involves an immediate response via the immune system. People with allergies to food can be diagnosed by blood tests (looking for IgE.) Allergies can develop even later in life (eg. crustaceans)
Intolerance to food does not involve an immune response at all. They are triggered by food chemicals which cause reactions by irritating nerve endings in different parts of the body.
As in Soystud's case of intolerance, the entire food group needed to be removed (removing the wheat protein alone was ineffective). This is because the chemicals involved in food intolerances are found in many different foods, so the approach involves identifying them and reducing intake of groups of food (ie grains.)
Testing for food intolerance with via immunoglobulin markers (such as IgG4) is pointless, as there is no immune involvement in intolerance. What those tests actually show, is which foods you eat the most. If you happen to be intolerant to a common food group, then the test will appear accurate, which is where the confusion arises.
www.ncbi.nlm.nih.gov/pubmed/18489614