RWP, you claim that the boundary which makes chemistry autonomous is this:
Physics/math deals with the physical and phenomenal whole - with universals such as physical laws, constants, geometry, mathematical structures and fields. Nothing determined by chemistry can exceed the "whole" of physics/math.
It is that whole into which the "whole" of "matter in all its motions" fits. Matter, for instance, is not yet even established in physics! Ordinary matter, some 5% of the critical density of the universe awaits the yet not found or made Higgs boson/field. And the Standard Model cannot explain dark matter (25%) or dark energy (70%)- thus the physicists even now pursue supersymmetry and extra dimensionality!
So if self-organizing complexity results in emergent properties which calls for new language to describe the autonomous entity (such as a car, water, betty boop) - the entity along with all its properites is nevertheless contained within the "whole" of physics/math.
But physics/math isn't the whole of "all that there is". The overarching principles into which physics/math fits are the subject of philosophy and theology.
Case in point: there is no physical causality in the void from which there is a beginning, e.g. of real space and real time.
It is like a concentric ring structure.
From the inner ring, betty boop is defined by the material contents of a set of space/time coordinates. From the ring of physics, she is defined by her intersection with the universals. But that's not all there is to betty boop! She is also a fractal of what lies "beyond" the "whole" of physics/math.