We study the interplay between coherent light-matter interactions and non-resonant pulse propagation effects when ultra-short pulses propagate in room-temperature quantum-dot (QD) semiconductor optical amplifiers (SOAs). The signatures observed on a pulse envelope after propagating in a transparent SOA, when coherent Rabi-oscillations are absent, highlight the contribution of two-photon absorption (TPA), and its accompanying Kerr-like effect, as well as of linear dispersion, to the modification of the pulse complex electric field profile. These effects are incorporated into our previously developed finite-difference time-domain comprehensive model that describes the interaction between the pulses and the QD SOA. The present, generalized, model is used to investigate the combined effect of coherent and non-resonant phenomena in the gain and absorption regimes of the QD SOA. It confirms that in the QD SOA we examined, linear dispersion in the presence of the Kerr-like effect causes pulse compression, which counteracts the pulse peak suppression due to TPA, and also modifies the patterns which the coherent Rabi-oscillations imprint on the pulse envelope under both gain and absorption conditions. The inclusion of these effects leads to a better fit with experiments and to a better understanding of the interplay among the various mechanisms so as to be able to better analyze more complex future experiments of coherent light-matter interaction induced by short pulses propagating along an SOA.