This study examines equifinality and compensatory calibration in hydrodynamic modelling of semi-enclosed coastal systems, using the Xiamen–Kinmen coastal waters as a representative tide-dominated case. A progressive diagnostic framework based on the normalized marginal contribution rate (MCR) was developed to quantify the relative effects of open-boundary forcing, spatially heterogeneous bottom friction, and atmospheric forcing within a depth-averaged barotropic model. Multi-metric validation against in situ water-level and depth-averaged current observations shows that the physical consistency of open-boundary forcing is the dominant control on model skill, particularly in reducing systematic elevation bias within the embayment. Bottom-friction parameterization produces more localized and site-dependent improvements, mainly affecting the spatial structure of current speed and direction under geomorphological constraints. Atmospheric forcing contributes only limited marginal gains during the study period, with modest directional corrections under weaker tidal conditions. These results indicate that hydrodynamic optimization for semi-enclosed bays should prioritize boundary consistency before local parameter tuning, thereby reducing compensatory calibration risk and improving physical interpretability. Remaining localized velocity errors in estuaries and high-curvature channels highlight the limitations of the depth-averaged barotropic assumption, under which density-driven baroclinic flows and vertical secondary circulations cannot be explicitly resolved. The proposed framework provides a reproducible approach for diagnosing and optimizing nearshore hydrodynamic models.