My dogs have eaten a couple of those foods over the years, too, but not in quantities that would make them ill.
A lot of the things on that list have killed plenty of dogs over the years. Just because a small amount hasn't killed any particular person's dogs, doesn't mean that a large amount hasn't killed plenty of others. Toxins can have very little effect, make you sick or kill you, depending on the amount ingested.
I think they did a pretty good job of trying to list whether only a large amount or regular feeding of something will cause illness or death, if it's a problem only if a particular food is fed raw or only if bones are cooked that's a problem. A couple of things are just not good for dogs and they also listed that. They didn't say that everything on the list would kill your dog or kill your dog in any amount.
Puppies have a very small body mass and dogs can be glutinous. That puts them at more risk for foods with a toxic component, if they get into things. A lot of people make their own dog food now and they might feed a particular food more excessively. Fortunately, most people that make their dog's food do a great job of reading the information that's available. Not everyone pours lots of bacon grease all over their dog's food every day.
I can't speak to the nutmeg or tomatoes, as I've never read about cases involving either of those foods. I've never seen a case at the vet's office when I worked there, either. If I had to guess, I'd guess that was a high volume issue, too.
The last time I checked, they hadn't identified the toxic component in the raisin/grape deaths, yet.
