APS does not begin by selecting Agency, Process, and Scale as three concepts presumed to be fundamental to all of biology. It begins with an explanatory problem: how does living organisation maintain and re-establish the conditions of its organised persistence through change?
That problem generates three distinguishable questions. Agency asks what the living system does in relation to the conditions of its viability. Process asks how organisational continuity is maintained through transformation over time. Scale asks across what spatial and temporal extents the organisation and dependencies relevant to that persistence are realised. Agency, Process, and Scale are therefore analytic projections selected because each exposes a different aspect of the explanatory problem APS addresses.
This does not mean that they are the only important concepts in biology, or that mechanism, information, energy, heredity, development, evolution, environment, function, and other biological concepts can be reduced to them. Nor does APS claim that Agency, Process, and Scale are the uniquely possible analytic framework for living systems.
The claim is narrower and testable: if organised persistence is the explanatory target, Agency, Process, and Scale provide a principled way of distinguishing what living systems do, how continuity is maintained through change, and across what extents the relevant organisation is realised.
Whether this architecture actually improves biological explanation cannot be established by its internal coherence. Its value must be demonstrated comparatively, against the strongest existing explanations of particular biological phenomena.