Fermented or cultured soy is better, easier to digest, and richer in enzymes. Examples are tempeh, miso, natto, traditonally brewed tamari or shoyu. Soy yogurt isn't technically cultured, but has cultures added, so it's kind of in between. As for limited quantities and the thyroid issue, I can only say there are differences depending on where you come from. Obviously, if you lived in most of Asia, soy is a predominant source of protein in both fermented and non-fermented forms.