1- k-points are not the same in all calculations. 2- If I were you, just for fun, I would try to make two calculations instead of three. In one of them (molecule+surface) the molecule is far away from the surface (make sure that vacuum in z-direction is large enough) and in the other one (molecule+surface) the molecule adsorbed on the surface. In this way both of your charged supercells will be the same size.
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