The Multi-Phase Transport model (AMPT) is used to study the effects of the parton-scattering cross-sections ($\sigma_{pp}$) and hadronic re-scattering on the linear contributions to the flow harmonic \fourth, the non-linear response coefficients, and the correlations between different order flow symmetry planes in Au+Au collisions at 200~GeV. The model results, which agree with current experimental measurements, indicate that the higher-order flow harmonics are sensitive to the $\sigma_{pp}$ variations. However, the non-linear response coefficients and the correlations between different order flow symmetry planes are $\sigma_{pp}$ independent. These results suggest that further detailed experimental measurements which span a broad range of collision systems and beam energies could serve as an additional constraint for the theoretical models' calculations.