Cross-isobath transport across continental shelf breaks connects coastal and deep-ocean waters, yet its estimation is complicated by sparse observations and vertically structured circulation. Using ROMS 4D-Var experiments for summer 2020 in the northern South China Sea, we compare simulations with and without shipboard CTD profiles and diagnose adjoint sensitivities of 72-h transport across a shelf-break section. The added CTD observations primarily modify the upper-ocean transport. During the 20-23 June target window, the upper 75 m transport difference reaches about 0.73 Sv, while the deeper-layer response is about -0.21 Sv, reducing the full-depth net response to about 0.52 Sv. Layer-resolved adjoint sensitivities show that velocity perturbations in the eddy and frontal region southwest of Taiwan tend to produce opposite-sign responses in the upper and deeper transport targets, indicating baroclinic compensation. In contrast, deeper velocity sensitivities are more concentrated near the continental slope and target section, where the two target layers respond more coherently, consistent with a slope-guided pathway. These results show that vertically integrated transport can obscure compensating responses in eddy-affected regions, while layer-resolved adjoints separate eddy-driven compensation from slope-coherent pathways. This framework provides a clearer dynamical interpretation of shelf-break exchange and more targeted guidance for future hydrographic and velocity observations.