You're creating straw dogs here. Nowhere did I speak of "will" of atoms, etc. Not sure where you are getting that. AND... they operate according to orderly principles. Things in the universe operate in a predictable manner - to the extent we understand these principles. There is no point in pursing that point of argumentation further except to highlight your words "what's built into it by nature in the first place."
Even our ability to make such distinctions as "order" and "chaos" bolsters the point of some idea of order and chaos. What we see as "chaos" is merely many items behaving according to said principles (i.e. what you've stated is "built into it by nature") in too great a volume or in too complex a path for our finite minds to process.