The stacking-dependent polarization and excitonic response of MoS₂/MoSe₂ heterostructures were investigated using GW+BSE many-body perturbation theory. While homobilayer MoS₂ exhibited a switchable interlayer dipole driven by registry-induced symmetry breaking, the MoS₂/MoSe₂ hetero-interface remained pinned by the intrinsic chemical potential mismatch between sulfur and selenium. In 2L-MoS₂/MoSe₂ trilayers, the stacking sequence enabled a deterministic control of photogenerated electrons between the central and bottom MoS₂ layers, governed by internal electric fields and quasiparticle band-edge shifts of 60–70 meV. Our calculations predicted a 36 meV interlayer excitonic shift, in remarkable agreement with recent experiments. These results elucidate the microscopic link between atomic registry and many-body interactions, establishing transition metal dichalcogenide trilayers as a potential platform for sliding ferroelectricity and programmable optoelectronic functionalities.