If you want to eat ancient grains I'd say go for it, but when I talk about whole grains I talk about what you're going to find in an average grocery store, and even what you find at a place like Whole Foods is pretty bad.
I highly suspect that nobody other than body builders are eating eggs in excess (if that's even possible -- what bad nutrients are in eggs?). Eggs are kind of a pain in the ass to cook (other than hard boiling), and most processing is about convenience.. In any case, things like choline are hard to get from other sources, and I think it's not that wild to assume our ancestors loved to raid birds nests for nutrient dense eggs.
Agreed on a lot of flip flops in dietary recommendations, but that definitely doesn't mean that the classic food pyramid was anywhere close to correct.