Actually, Dr. Davis has asserted elsewhere that the current method of gene splicing is much less dangerous than the breeding of wheat that occurred beforehand. Agriculturists had the best of intents, creating modern wheat from its 4-and-a-half foot tall ancestor in Grandma’s day by first breeding it to have a bigger head with more seeds, then breeding it for a shorter stalk in order to keep that heavier head from breaking the plant.
However, modern wheat has numerous odd proteins in it, including ones that break down into chemicals that can latch onto opium receptors in the brain. That way, if you decide to quit wheat, you can actually go through a sort of withdrawal.
Furthermore, the wheat is full of an easily digestible carb called amylopectin — less digestible versions of it are in potatoes and beans. So eating wheat will cause a spike in your blood glucose as all that amylopectin is digested. Insulin is subsequently produced, causing that glucose to be stored as fat. So people who eat a lot of wheat will inevitably gain weight.
Wheat can also exacerbate asthma and certain allergies. I’m guessing it’s because of other noxious proteins in this plant. When I first drastically reduced my wheat intake, I found myself sneezing a lot less, and my hay fever didn’t bother me as much, although I always seem to have one week out of the year when it still does. I also lost weight.
Wheat is a common staple, and unfortunately, it is recommended by the government. However, regular consumption of it does leave a lot of, shall we say, usually-non-deadly collateral damage in people.
I would say that the wheat proteins end up suffering the same fate as the majority of other proteins we eat. Being plant proteins, they are less easy to digest, so I would expect larger polypeptides to remain after the digestion process--but they would be excreted in the feces or consumed by gut bacteria, just like everything else we eat.
The overconsumption of carbohydrates is a problem. Just plain eating an unbalanced diet is a problem. Beyond that, there are no magic diets that have all the magical ingredients. You get enough of the micro- and macro-nutrients, or you don't. That is basically the essence of what decades of nutritional research have revealed.