Establishing a rigorous nexus among reference-clock modeling, timing compensation, and system-level performance is imperative for cislunar positioning, navigation, and timing (PNT) architectures. In this study, we propose an integrated analytical framework to bridge relativistic clock definitions with PNT requirement allocations. Rather than treating timing budgets in isolation, the framework sequentially couples a first-order weak-field Earth–Moon clock difference model—which captures a temporal accumulation of approximately 20.48 ms annually—with chronological validations of empirical forecasting strategies. Furthermore, by propagating compensation residuals through a four-state nav-estimator, we demystify the assumption that residual timing translates linearly into position degradation. Crucially, we demonstrate that timing requirements in cislunar space are inextricably bound to source-dependent residual components, geometric dilution, and the overarching non-timing error floor, thereby mandating a joint geometric-stochastic budgeting paradigm for future lunar constellation designs.