The Robb Wolf 'The Paleo Solution' is very interesting on this. He says that since farming was only introduced in the Neolithic era about 5-10,000 years ago, our bodies have not evolved to cope with the modern grain-heavy diet.
So I think a problem with this is that evolution in diet changes have been shown in numerous populations more rapidly than this - the indigenous populations of the arctic have typically only been there for half that time at most, but have significant adaptations to their very different diets (very meat based etc.)
And of course the gene for lactose digestion in adults has been identified and been around for thousands of years, that also goes back to the same 5-10,000 for grain. So if dairy and grain happened at the same time, and the vast majority of Europeans have adapted to dairy - why would it be different for grains?
Also remember that processed seed consumption almost certainly predates modern farming as you suggest (the 5-10,000 years) there's plenty of stone age suggestions of such processing going on, just on wild grasses rather than tilled fields.
Of course all that really shows is that the rationalisation of why something works is almost certainly wrong, it doesn't necessarily change the fact that it may work. However personally I'd like a real explanation and genuine science journals, and not pop-science books.