Extensive soft x-ray photoelectron spectroscopy studies are performed on Ba8Ga16Ge30 (BGG) and Sr8Ga16Ge30 (SGG) single crystals ranging from Fermi to core levels, at a high-energy facility. Valence band x-ray photoelectron spectroscopy (XPS) experiments with theoretical calculations revealed that the valence band is mainly constructed by the Ge/Ga 4s and 4p wave functions with little contribution of the Ba/Sr atomic orbitals. Surprisingly, unexpected features evidencing the different shift for the 2a- and 6d- sites between Ba 4d and Sr 3d are observed. The detailed analyses including theoretical support by first-principles band-structure calculations lead to the conclusion that the component distributions of the larger tetrakaidecahedral cage are different depending on the endohedral atoms, which contrasts with the past consensus that BGG and SGG have the same framework structure. This may give thorough reconsiderations on earlier interpretations of experimental data.