We demonstrate that the lattice formation of an adsorbed molecule decouples the molecule-substrate interaction to change the Kondo resonance, which occurs due to interactions between conduction electrons and the molecule's unpaired spin. The double-decker bis(phthalocyaninato)terbium(III) complex, which is single-molecule magnet and forms a Kondo resonance on a Au(111) surface through an unpaired π-radical spin, is studied using scanning tunneling microscopy/spectroscopy (STM/STS). In the STS spectra, an unusual sharp, strong peak (peak A) is found only for the molecule in a film. The peak position of peak A (εA) cyclically shifts by several hundred millivolts as the STS tip position shifts along the outer circle of the molecule, reflecting the tilting of the upper phthalocyanine (Pc) ligand from the flat-lying lower Pc ligand. The Kondo resonance, which is detected as a sharp peak at the Fermi level, also shows cyclic variations of the peak width and intensity. As εA approaches EF, the Kondo temperature (TK) increases. We propose a model that peak A originates from the singly occupied molecular orbital state whose energy is shifted by an unscreened final state effect due to a decrease in the molecule-substrate chemisorptive interaction. We further examine this model using density functional theory calculations, confirming a decreased molecule-substrate interaction for molecules in the film compared to that of isolated molecules. Further calculations of a tilted upper Pc ligand configuration show a site-dependent, cyclic variation of the molecule-substrate interaction within a molecule.