For the sake of debate and bare in mind you've agreed with the following statement: we've eaten pretty much everything that didn't kill us for a million years when we hunted and foraged.
Why then do we have so many food issues now? In part, tying in with your second statement (which I mostly agree with), it's down to additives. One which I really dislike is Glucose Syrup which seems to be in everything adding a little sweetness. we NEVER add it to scratch cooked food but it's in a ton of pre-made meals.
The other, which has been looked at and tied in with allergies, is a lack of exposure early on. The kids that were exposed to a LITTLE peanut in their formative years are far less likely to have peanut allergies. I'd say the same can be said of intolerances.
Now, all that said, it can come down to amounts. I, for one, eat very little bread. If you're having doughnuts, burgers in a bun and a lot of cookies and cakes then yeah you're gonna be getting a good amount of gluten.