The competition between intermolecular interactions and lateral variations in the molecule-substrate interactions has been studied by scanning tunneling microscopy (STM), comparing the phase formation of (sub-)monolayers of the organic molecule 2,4'-BTP on buckled graphene/Ru(0001) and Ag(111) oriented thin films on Ru(0001). On the Ag films the molecules form a densely packed 2D structure, while on graphene/Ru(0001) only the areas between the maxima are populated. The findings are rationalized by a high corrugation in the adsorption potential for 2,4'-BTP molecules on graphene/Ru(0001). These findings are supported by temperature programmed desorption (TPD) experiments and theoretical results.