We report on the epitaxial growth, theoretical modeling, and structural as well as optical investigation of multi-layer, site-controlled quantum dots fabricated using the buried stressor method. This deterministic growth technique utilizes the strain from a partially oxidized AlAs layer to induce site-selective nucleation of InGaAs quantum dots. By implementing strain-induced spectral nano-engineering, we achieve spectral control of emission and a local increase in the emitter density. Furthermore, we achieve a threefold increase in the optical intensity and reduce the inhomogeneous broadening of the ensemble emission by 20% via stacking three layers of site-controlled emitters, which is valuable for using the SCQDs as a gain medium in microlaser applications. Our optimization of site-controlled growth of quantum dots enables the development of high-β microlasers with increased confinement factor.