What Pollan actually advocates is eating a traditional diet that has been refined over centuries. He says that which one you pick doesn't matter that much.
The traditional diets of people living around the Mediterranean and people living near the Arctic circle have nothing in common, but according to Pollan, either will give you better health outcomes than a normal Western diet.
If people have been eating a certain way over a long period of time, they have probably learned to avoid the stuff that will kill or injure you, and probably have discovered foods that nutritionally complement each other, as well. (He gave examples of such complementary foods in traditional diets, which I can't remember right now.)
One thing I've definitely noticed time and again is how complete traditional diets tend to be. It's amazing, thousands of years ago, with no concept at all of nutrition, people managed to put together fantastically complete (and tasty) diets.
I can't tell if you're being really subtle here, but the causality is probably reversed - people ate whatever they could get away with, and over the course of many tens of thousands of years they evolved to process that food efficiently. Anatomically modern humans evolved approximately 200,000 years ago, and agriculture was only invented 10,000 years ago. And industrially produced processed food didn't become a staple of most Westerners' diets until 65 years ago.
The skills necessary to survive on the local available food in one place don't entirely translate someplace else. Somebody had to look at a squid for the first time and decide to eat it for example. Or that the rotting month old cabbage would be a good meal.
Traditional foods are often preagrarian foods in some cases. You can find expensive wild foods restaurants in South Korea for example that serve only food you can gather in the mountains, mushrooms, pine nuts, pine needles, ferns, wild onions, etc. These are things that people cobbled together before they had any knowledge at all of nutrition and amazingly, when we look at them today with the modern eye find out that they represent a fantastically complete diet, rich in essential nutrients. In Latin America you can still find plenty of pre-Columbian cuisine with similar characteristics. And I'd wager elsewhere as well.
Put another way, why didn't they just settle on say mushrooms? How come the entire diet for a people isn't just one food? Or a combination of foods that represent a diet lacking in a certain vitamin? Amazingly, wherever you go, the traditional foods tend to make up a complete diet.
It seems a modern curse that we can gorge ourselves on singular foods and grow fat and suffer malnutrition at the same time. Only today can somebody eat hamburgers and pizza 3 times a day for years.
Or you can just eat the actual plants and animals and be done with it.
You don't just grab a potato out of the ground and eat it whole. Or jump out into a field of cattle with a fork and knife ready to go. You can do that with some foods, not so much with others. If the metric is "you must be able to eat it right out of the wild with 0 processing" you're going to eat a lot of raw tomatoes and peppers and not a whole lot else.
In many cases, you have to process the food source to make it edible. Rhubarb for example has poisonous leaves that will kill you. The green bits of the tomato can surpress cardiac functions. For most animals you can't just start biting chunks out of them. You may have to remove internal organs that are inedible, bones (I don't see many paleo eaters advocating cracking open thigh bones to get at the marrow very often btw), etc.
http://www.environmentalgraffiti.com/news-10-poisonous-fruit...
In some cases, edible parts may contain bad stuff, pork meat for example is well known to be unsafe raw. I'm pretty sure cavemen ate pigs (or at least boar). Cow brains may contain prions. etc.
I do agree with you that food manufacture from chemical components on up is likely not complete, but there's not really much of that in the industry. Even highly "processed" foods like hotdogs or McDonald's chicken McNuggets are just ground up and cooked scrap meat and connective tissue (all paleo friendly!). They have all the stuff that's in meat anyways. The process to make imitation cheese doesn't generally fall under that kind of manufacturing process.
Many common and cheap foodstuffs also don't contain much nutrition. Vitamin fortified rice has probably improved the lives of a billion people.
People also get all kinds of scared when the chemical names for common food components are used. Should I use "salt" or "sodium chloride"? Should I avoid all foods with Monosodium Glutamate (good luck with that)?
But like anything it all just comes down to moderation. Nutmeg is great and natural, but if you eat too much of it you'll get have hallucinations and may die. Who knows what's in a clam, perhaps if you eat clams 3 times a day for a year (a completely possible scenario for a caveman) you'll have serious health problems like mercury poisoning or some other issue.
Who knows?
and there is probably stuff in the part you are throwing away that is good for you.
You may also be throwing out stuff that's very bad for you. It's all conjecture.