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 Rabioscillations 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 nonresonant 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.