This smacks of "security through obscurity" to me. Windows has been thoroughly reverse-engineered by black-, gray- and white-hats: is there a single windows .dll, .sys or other component whose purpose is remains a mystery or cannot be subverted by a person with physical access?

It is. Any anti-cheat system that relies on having explicit control of the client is inherently flawed, but it is considered "good enough" by most people.