With regards to dairy, it's more about a person's individual reaction to it. It's a similar argument with nutrient density (since milk is intended for growing offspring, obviously it's going to be very nutrient dense). The downside is potential inflammation or not having the enzymes to process it.
I would definitely not lump eggs and dairy as "bad" in any way though.
Also, the "cholesterol" thing is a very bad thing to focus on. Cholesterol is not bad! You need cholesterol. (What do you think cell membranes are partially composed of?
Whole grains are not as good as you think. Often, they're made from strains that are optimized for growing and robustness not nutrition. Also, unless you're exercising a lot you really don't need much in the way of carbs.
As far as eggs and dairy go, sure they are healthy for who is meant to be consuming them - baby chickens and baby mammals, but that doesn't mean they are good for us in excess.
There have been, and continue to be, so may flip flops in dietary recommendations and what is good/bad for you, that it seems common sense is a better approach. All things in moderation, and indeed look to what our relatively recent ancestors have been eating to get an idea of what our bodies are evolved to eat - whole foods and not processed ones and chemical additives.
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.
There is also not a very strong connection between dietary cholesterol and serum levels, anyway.
20,000 years maybe yes. But we have not been agricultural for that long. And that's why grain-based food still is not something we're well adapted to.
Your body produces cholesterol naturally, without any meat or dairy. In my case it actually produces way more than I need, even on a vegan diet, because of genetic factors. People should test their LDL and evaluate whether eating cholesterol is healthy _for themselves_ as it’s different for everyone.