(Abridged) Classification schemes for YSOs are based on evaluating the degree of dissipation of the surrounding envelope, whose main effects are the extinction of the optical radiation from the central YSO and re-emission in the far-infrared. Since extinction is a property of column density along the line of sight, the presence of a protoplanetary disk may lead to a misclassification when the system is viewed edge-on. We performed radiative transfer calculations, using the axysimmetric 3D radiative transfer codes RADMC and RADICAL, to show the effects of different geometries on the main indicators of YSO evolutionary stage, like the slope of the flux between 2 and 24mum, the bolometric temperature and the optical depth of silicates and ices. We show that for systems viewed at intermediate angles the classical indicators of evolution accurately trace the envelope column density, and they all agree with each other. On the other hand, edge-on system are misclassified for inclinations larger than ~65deg. In particular, silicate emission, typical of pre-main sequence stars with disks, turns into absorption when the disk column density reaches 1e22cm-2, corresponding e.g. to a 5e-3 Msun flaring disk viewed at 64deg. A similar effect is noticed in all the other classification indicators studied alpha, Tbol, and the H2O and CO2 ices absorption strengths. This misclassification has a big impact on the nature of the flat-spectrum sources (alpha ~0), whose number can be explained by simple geometrical arguments without invoking evolution. A reliable classification scheme using a minimal number of observations is constituted by observations of the mm-flux with both a single dish and an interferometer.
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