Yoga works because of physics and the logic, order, and predictability of the Universe. Yoga or shall I clarify this by saying, “Real Yoga” is a Spiritual Science (8 essential stages codified by Patajalis) and clear instruction to become a human in the adult state, or a whole person, or an enlightened individual– the term was called apotheosis (the process of the human becoming divine). The major principle that Yoga is founded on is “how we think is what we become” but initially the conscious mind is small and the physical body is attached to duality (the physical and mental dimensions) which produces a limited perspective of the individual. Yoga is a practice that educates the individual in how to separate from the physical/mental worlds and connect to a more subtle resource of sustenance (Prana, Chi, God, Void, Nothing etc.– call it what you want) which impregnates the seed of the conscious mind. This internal connection (Yoga) is what initiates a process that unfolds in three phases– unconscious awareness, to self conscious awareness to super conscious awareness. From this newly achieved position the individual is now becoming the creator of their reality.
However, when Yoga is diluted, watered down, or modified it can have good results because of the placebo effect– remember “how we think is what we become.” Thought is an energy capable of producing affects but it is measurable by the amount of strength it is emitted with. It is belief that gives thought the power of intention. Just like there is a difference between Healing and Curing there is a difference between the placebo effect and conscious control. In fact, the origins of the word heal means whole, when the mind is small we feel like victims but when the mind is open and the body is connected to something pure, powerful and sacred the thoughts have power to create.
The physics of Spirituality is like attracts like and two things can’t occupy the same space at the same time. When the physical body is attached to particles and waves (physical and mental realities or duality) which is fear and limitation— that’s what we become (small minded). When the body is purified (shaucha) and literally rebirthed in the Life Force or Prana (the unified field is truth and wholeness), then we become truth and wholeness or Spirit. Yoga is instruction to become a whole person with an open mind.

Yes, the physical body is a diagram of the mind but the mind isn’t limited to the physical body and the chakra system is a diagram of the mind which transcends physical limitations. We are thinking on many levels and in order to be able to make changes on all of these levels we must transcend the body and open the mind but the only way to do this– is union with Prana; then you have “Real Yoga” and clear understanding in how it works.