The semiconductor industry has adopted heterogeneous integration (HI), incorporating modular intellectual property (IP) blocks (chiplets) into a unified system-in-package (SiP) to overcome the slowdown in Moore's Law and Dennard scaling and to respond to the increasing demand for advanced integrated circuits (ICs). Despite the manifold benefits of HI, such as enhanced performance, reduced area overhead, and improved yield, this transformation has also led to security vulnerabilities in the SiP supply chain and in-field operations, ranging from chiplet piracy and SiP reverse engineering (RE) to information leakage. Although conventional countermeasures provide the desired robustness for monolithic ICs, they are insufficient for addressing these challenges in the context of HI. To address these concerns, this paper presents a novel root-of-trust architecture, augmenting the process of integration using a centralized chiplet hardware security module (CHSM), aiming to provide comprehensive and robust protection throughout the SiP supply chain and in-field operations. Also, the proposed architecture equipped with the CHSM effectively addresses potential security breaches while providing robust protection against zero-day attacks through its reconfigurable capabilities. Throughout five detailed case studies, this paper performs a comprehensive security analysis to illustrate the resilience of CHSM against contemporary attack scenarios in the HI domain.