This is a great question. First, the Food and Drug Administration has set forth guidelines related to the use of GMOs, and in those documents they reference the science that indicates food developed through biotechnology are digested in the same manner as other foods and therefore provide the same nutrition, or in some cases more nutrition (if the goal of the biotechnology was to enhance nutrient content). The science also indicates that these foods are safe for consumption and that they are not contributors to increased allergies.
With regard to your question about allergens, the guidelines for development of GMOs require that if any food that could be an allergen is introduced into a food that would not normally carry that allergen, then the food must provide that declaration. The FDA also requires that scientific evidence support the fact that no potential allergen was introduced into the GM product. The goal of these guidelines is to prevent allergic reactions.