Thanks to an experimental (in situ reflection high-energy electron diffraction and ex situ high-resolution electron microscopy) and a theoretical probabilistic cellular automaton study of surface kinetic roughening in low temperature silicon molecular beam epitaxy, we achieve a clear correlation between the surface roughness and the microscopic morphology of the growing layer. A transition in the growth mechanisms between a perfect epitaxy regime and another one displaying structural defects is shown. It may explain previous unusually observed deviations of the surface roughness scaling behavior unpreviewed by current theories. The effect of gallium atoms as "surfactants" is also investigated. High-resolution electron microscopy comparison of layers grown with and without gallium shows its role in the surface morphology smoothing.