This has been somewhat understood for sometime, though the science on how phytoestrogens actually react with the human body isn't well understood. The article also doesn't make it clear that there are differences in various soy-based foods. The process that produces tofu (roughly equivalent to making cheese from milk) breaks down the hormone-like compounds, while more raw forms of soy (soy milk, various soy-based meat and dairy alternatives, whole soy beans, etc.) still contain those chemicals.
The interesting thing about soy, to me, is that it is one of the marketing miracles of our time. It was considered inedible in western culture until just the current generation, and now it is considered a "healthy" addition to just about any food. It was used for oil and other raw materials in industry, but not for food. While not as successful as corn (which is simply unavoidable in American foods), the soy industry has integrated its products into the daily diet of almost everyone. While I eat fresh tofu several times a week, I avoid mass-market foods that contain soy, and anything that contains soy in its various "raw" forms (soy flour/meal, soy milk, or whole soy beans). Soy sauce is problematic, as there are "quick ferment" processes used in most cheap soy sauce brands that do not break down the suspect compounds...properly slow fermented soy sauce is generally fine, though.
Traditional tempeh is fermented, and so is generally quite friendly. Tofu, as I mentioned, is basically soy milk curd.
But most instances, in US groceries, where something contains "soy protein" it's going to be in the form of soy flour, or soy milk (which is generally soy flour, water, sugar), which, unless fermented for soy sauce and tempeh or made into tofu, has phytoestrogens to one degree or another.
I've never actually found good data on this topic, and it's an area of interest since I'm vegetarian. I enjoy some of the soy-based meat alternatives (Boca Burgers, Morning Star Farms products, etc.), but many contain soy (as well as wheat gluten) in forms that are poorly defined, so I suspect they are subject to this problem. I generally avoid them for that reason. I'd be curious to know what processes do break down those compounds, if any others besides fermentation and turning into tofu do. Simply cooking seemingly does not, however.
The interesting thing about soy, to me, is that it is one of the marketing miracles of our time. It was considered inedible in western culture until just the current generation, and now it is considered a "healthy" addition to just about any food. It was used for oil and other raw materials in industry, but not for food. While not as successful as corn (which is simply unavoidable in American foods), the soy industry has integrated its products into the daily diet of almost everyone. While I eat fresh tofu several times a week, I avoid mass-market foods that contain soy, and anything that contains soy in its various "raw" forms (soy flour/meal, soy milk, or whole soy beans). Soy sauce is problematic, as there are "quick ferment" processes used in most cheap soy sauce brands that do not break down the suspect compounds...properly slow fermented soy sauce is generally fine, though.