Oats, yes. Tofu and beans, yes. I think I recall that Paleo doesn't like even green beans. But Sisson eats them.
Tomatoes are fine, pumpkin is fine, berries are fine. The problem with oranges and some other fruits is the gylcemic response. With yogurt, he wants you to be careful of how it's made. I think he thinks more people have trouble with dairy products than they think.
There are lots of warnings in the book about pesticide use and thin skinned fruit/veg.
So my interpretation would be to skip the oats and tofu. That's all.
I am into my 3rd week now of no sugar, dairy, processed foods, and very little wheat products, and I must admit, I feel incredibly awesome. I am also doing ESE, and my wife gave it a try this past weekend, and she really liked it as well.
I bought 'The Paleo Diet' from amazon, and devoured it in one day, but I found the diet too restrictive. For instance, I cannot eat peanut butter, nor beans. Here in Costa Rica, rice/beans are a staple food, usually eaten at every meal, and frankly, I enjoy eating beans. But I'm keeping my diet as natural as I can.
I know, right? Under Paleo, I would've had to limit myself on eggs and green beans, and just completely eliminate too many other foods. It was just entirely too restrictive. It was a pretty decent read though.
Sugar and grains (even the healthy ones) can act like a poison at certain levels. Too much of a good thing, is not a good thing. There are many substances that are safe, beneficial or even necessary in some amount, and toxic at another. Even water is toxic in excess (it takes a lot to reach that level of excess, but it's possible).
Minerals, and fat soluble vitamins are good examples. Necessary in small amounts, and toxic in large amounts.
Oxalic acid is another, many fruits and vegetables contain this "poison," but only in large doses is it dangerous. Rhubarb leaves are considered poisonous because of the large concentration of oxalic acid. Rhurbarb stems (the edible portion) contain oxalic acid too, but you'd have to eat pounds and pounds of the stuff to get sick. Tea leaves can be as "poisonous" as rhubarb leaves, but the concentration in tea is too small to be dangerous. Eating a significant amount of tea leaves could be, though.
How much is too much, is going to be the hardest truth to pin down, because I think it does vary tremendously, not only because of a person's unique metabolic situation, but also other variables that aren't always easy to measure.
I've felt so good on an essentially grain-free diet, that I do look at grains much differently now. Rice is the only grain I eat regularly, and even then not daily or even weekly. If I eat grains more than a few times a week, I tend to have more flares of my autoimmune symptoms. I have to avoid wheat entirely (I suspect an actual allergy, but can't have allergy testing right now because one of my medications would make testing dangerous).
For some reason, "too much of a good thing" seems to be a difficult concept for people to grasp. "If a little is good, a truckload must be even better," seems to be the prevailing attitude. I think it's why virtually everything in a package contains some kind of warning on it (usually against something so stupid, I can't believe anyone benefits from the warning - doesn't everyone already know that operating a curling iron in the shower is a bad idea?)
As a diabetic with IBS, I can definitely attest to the fact that "too much fruit," really can have consequences that are best described as "toxic." And you don't have to have intestinal disorders or be diabetic to experience these effects. Too much fruit might be very different for one person than another. Without health issues such as obesity, blood sugar issues, intestinal or digestive issues, IBS - a person's "too much" might be 12 pieces of fruit instead of 3.
I don't like that so many diet and nutrtion books want to break eating down to a list of allowed and forbidden foods, but the alternative is one that isn't very popular. Learning more about nutrition to the point of being able to understand and create balance, and to identify and address specific nutritional needs is not rocket science, but it is more effort than most people want to put in. If the entire topic cannot be exhausted in one easy-to-read, relatively short book, most people aren't interested.
You can't reduce such a complicated topic into a two page article (ideally with pictures), but anything longer than that and you lose the interest of more readers than not.
Folks here on 3FC seem to be the exception to this rule (which is why I love hanging out here).