In its present state, the Amplification Factor Transport (AFT) model provides an efficient alternative for high-fidelity stability methods for complex geometries subject to low-speed conditions considered in the industrial-production CFD environment. Its performance has not yet been documented for the typical transition scenarios in hypersonic conditions. The goal of the present study is to apply the AFT model to a yawed- and flared-cone configuration, for which the laminar flows respectively support the crossflow and second-mode instability mechanisms, and to compare the amplification results against high-fidelity results computed with Linear Parabolized Stability Equations (LPSE). High-resolution viscous-flow solutions are provided with OVERFLOW and COFFE. For the yawed-cone case, the AFT model yields the largest amplification in a region of the flow where the expected crossflow instability is not amplified (in the leeward symmetry plane) according to LPSE. For the flared-cone case with a wall-temperature slightly lower than the adiabatic value, the AFT model yields extremely large amplification factors (in excess of 100), exceeding the computed LPSE amplification of secondmode instability results by a factor 14. Upon considering a cold-wall condition, the model shows much smaller amplification factors, which is the opposite with respect to the expected behavior of the second mode. The AFT model does not adequately capture the crossflow and second-mode instability mechanisms in its present state.