We hypothesized that in the open forms of diphenyl-substituted photochromic compounds, immediately after the photoinduced cleavage of the C-O bond, one of the phenyl rings forms a stack with an aromatic system at the other end of the alkyl linker. The formation of these intramolecular stacking excimers is made possible by a known increase in the rotational mobility of the linker double bonds in the excited state. The flexibilities of linkers are analyzed in terms of changes in their dihedral angles. After internal conversion, stacking is partially broken but it still prevents the recovery of the C-O bond. This explains the significantly greater stability of the open forms of diphenyl-substituted benzopyran and naphthopyran compared to dimethyl-substituted ones. Open structures with residual stacking are intermediate and by thermal motion, they transform into stable trans-trans and cis-trans forms. However, in our opinion, they significantly affect the equilibrium of closed and open isomers in solution. In particular, the calculated stacking energy of 2H-naphthopyran turned out to be higher than that of 3H-naphthopyran, which partly explains the significantly greater stability of the open form of the former. For the DFT/TD-DFT calculations performed in this work, the following functionals were selected to provide reliable stacking for the open forms of all three studied compounds: APFD, M052X, M06HF, as well as B3LYP with D3(BJ) Grimme dispersion correction. The 6-311++G(d,p) basis set and cyclohexane solvent modeled using IEFPCM were also used.