The inherent relationship between the state of the boundary layer, aerodynamic heating, and surface conditions make the potential for interaction between the structural response and boundary layer transition an important and challenging area of study in high speed flows. This paper phenomenologically explores this interaction using a fundamental aerothermoelastic model. Specifically, an existing model is extended to examine the impact of transition onset location, transition length and transitional overshoot on the structural response of surface panels. Transitional flow conditions are found to yield significantly increased thermal gradients, and can result in higher maximum panel temperatures compared to turbulent flow. Results indicate that accounting for transitional overshoot in heat flux and fluctuating pressure reduces the flutter onset time relative to no overshoot. Temperature-dependent material properties are found to cause dips in the flutter onset time for a subset of transitional flows. Furthermore, overshoot occurring near the mid-chord can yield average temperatures and peak displacements exceeding that experienced by the panel subject to turbulent flow. These results suggest that fully turbulent flow does not always conservatively predict the thermo-structural response of surface panels.