Decentralised manufacturing is expanding as digitally controlled fabrication tools become accessible to SMEs, independent operators, and community workshops outside traditional factory settings, but the resulting heterogeneous, autonomously operated network introduces systemic uncertainty that no central authority governs. This paper proposes a systems-theoretic framework in which Free and Open Source Software (FOSS) governance acts as the structural interoperability layer of a distributed cyber-physical manufacturing system (CPS), and node-local digital twins --- each hosting a machine learning (ML) disturbance estimator --- provide local adaptive compensation without centralised data aggregation. A defining property of the architecture is automatic improvement propagation: learned corrections distribute via federated learning to structurally similar nodes without operator intervention, and the open, observable FOSS ecosystem enables advances in one fabrication modality to transfer to others through shared interface standards. The framework is applied analytically to three disturbance classes: regulatory restriction, technical process variability, and supply-chain disruption. Across cases, the analysis shows how open modular interfaces and local adaptation preserve functional continuity under perturbations that would more strongly affect centralised architectures. The contribution is a unified mathematical basis for robustness analysis in decentralised manufacturing CPS and a foundation for future simulation and empirical validation.