In natural foods, there are other substances that balance out the harm, making it healthy overall. These other substances are absent when it's used as an additive.
Indigenous people processed acorns to remove tanins.
Kidney beans (and many other legumes to variably lesser degree) naturally contain phytohaemagglutinins (PHA-E) which cause red blood cells to clump together. These can be reduces several orders of magnitude by repeated cooking, washing, and draining.
Men shouldn't eat too much soy or chia seeds. Small amounts of chia seeds are fine.
Most adults are lactose intolerant unless they have lactase persistence genes.
Spinach, pepper (the spice kind), rhubarb, almonds, and more contain oxalate that can lead to kidney stone formation. Excess vitamin C does also. Increasing citrate intake helps prevent calcium kidney stone formation, but doesn't help with oxalate kidney stones as much.
The list of antinutrients is long. Don't overdo eating one "natural" ingredient or another because that's the greatest risk of becoming a Chubbyemu video subject.
It's better to eat things in moderation and know what antinutrients are in what foods. There are tradeoffs.