Dithiol self-assembled molecular layers (SAMs) are exploited as controllable spacers between CdSe light absorbers and a gold collector. Using two sets of molecules, alkanes with different chain lengths and biphenyl derivatives with varied conjugation, the charge transport across corresponding SAMs is investigated by chemically resolved electrical measurements and photoluminescence (PL). Complementarity is found between the photovoltage and the PL intensity as a function of spacer thickness. However, it is not obeyed for varied conjugation, a feature shown to arise from reduced charge selectivity in the transport efficiencies. Interplay between dark and photo-induced mechanisms are revealed, where the emergence of charge traps by itself becomes spacer dependent via a remote effect of the substrate on surface chemical activity.