I'm not sure of the exact mechanisms involved, but I'm incliined to agree that our digestive tracts have a hard time digesting raw grains. My theory is that it's because the fibers have not been hydolyzed or softened.
Nonetheless, just because we can't digest grains well in their raw form, doesn't mean that they shouldn't be eaten at all. We don't digest eggs well in thier raw form, either. So what do we do? Cook them. Cooking, soaking, and sprouting are not always evil processing methods. Cooking some foods, such as legumes, makes them nutritionally sound for humans to eat. The protein is more available because protease inhibitors are destroyed, the starch is gelatinized, and potentially toxic substances such as hemagglutinins that make red blood cells stick together, are destroyed, as well. Sprouts are highly concentrated sources of vitamins and minerals.
Refined grains suck, I agree, but whole grains are still fine to eat and should be eaten. Phytates do bind to minerals, but so do oxalates in rhubarb and spinach. Surely, you wouldn't reject spinach (a "superfood")because of oxalate. Some fibers bind to minerals, too, but of course, fiber is essential for digestional health. In addition, minerals themselves interact with each other; high sodium causes both calcium and sodium to be excreted when sodium levels are high, and magnesium and phosphorous bind to each other in the digestive tract. No one would avoid these minerals just because they react with each other. The risk of mineral deficiency from all of these circumstances is minimal when mineral intake is adequate.
As for the acidity of grains: Grains are by far not the only acidic food. Fruits, milk and milk products, and other proteins are acidic, too, but none of them should be excluded from the diet on that basis. It all comes down to balancing the acids and bases. (By the way, did anyone else wonder how fruit juices are listed as basic in the chart in Berardi's "Covering You Acids and Bases?" Did I miss something? I've tested the pH of several of those juices myself, and they were all acidic.)
As a further note to ponder, grains are the staple in the diet of most populations. They supply the majority of kcalories and half the protein (gasp!). Like it or not, they have made the continuation of humankind possible.