(abridged) The calculation of the thermal stratification in the superadiabatic layers of stellar models with convective envelopes is a long standing problem of stellar astrophysics, and has a major impact on predicted observational properties like radius and effective temperature. The Mixing Length Theory, almost universally used to model the superadiabatic convective layers, contains effectively one free parameter to be calibrated --alpha(ml)-- whose value controls the resulting effective temperature. Here we present the first self-consistent stellar evolution models calculated by employing the atmospheric temperature stratification, Rosseland opacities, and calibrated variable alpha(ml) (dependent on effective temperature and surface gravity) from a large suite of three-dimensional radiation hydrodynamics simulations of stellar convective envelopes and atmospheres for solar stellar composition (Trampedach et al. 2013). From our calculations (with the same composition of the radiation hydrodynamics simulations), we find that the effective temperatures of models with the hydro-calibrated variable alpha(ml) display only minor differences, by at most ~30-50 K, compared to models calculated at constant solar alpha(ml). The depth of the convective regions is essentially the same in both cases. We have also analyzed the role played by the hydro-calibrated T(tau) relationships in determining the evolution of the model effective temperatures, when compared to alternative T(tau) relationships often used in stellar model computations. The choice of the T(tau) can have a larger impact than the use of a variable alpha(ml) compared to a constant solar value. We found that the solar semi-empirical T(tau) by Vernazza et al. (1981) provides stellar model effective temperatures that agree quite well with the results with the hydro-calibrated relationships.