Laminar-turbulent transition is a critical determinant of aerodynamic heating and skin friction for hypersonic vehicles. Predicting this process requires high-fidelity numerical methods capable of resolving delicate disturbance waves within the boundary layer. This paper presents a unified high-order numerical platform that extends the shock-fitting (S-F) methodology to multi-block structured grids, specifically designed for complex, finite-span 3D geometries at non-zero angles of attack. The platform’s primary strength lies in its hybrid simulation capability. For late-stage transition and shock-disturbance interactions, the 3D unsteady nonlinear S-F solver is employed to capture the full physics of nonlinear disturbance evolution without the numerical dissipation typical of shock-capturing schemes. Conversely, for the analysis of small-amplitude disturbances, the platform integrates a Linearized Navier-Stokes (LNS) solver. By linearizing the governing equations around a steady-state base flow, the LNS approach bypasses the costly calculation of nonlinear interactions. This provides a high-fidelity, low-cost alternative that significantly reduces CPU-hour requirements while maintaining machine-level precision through the use of the TAPENADE automatic differentiation (AD) engine. This integrated framework allows for an exhaustive characterization of transition mechanisms, such as crossflow instabilities and Görtler vortices, under realistic flight conditions. By combining the rigorous accuracy of nonlinear S-F simulations with the computational efficiency of the AD-enhanced LNS solver, the platform bridges the gap between theoretical stability analysis and practical hypersonic aerodynamic design. The numerical results are validated against established experimental data, demonstrating the platform's robustness and efficiency in predicting transition for authentic 3D configurations.