The flexibility of metal-organic frameworks (MOFs) featuring stimuli-responsive structural transitions is often governed not only by the chemical composition and topology but also by orthogonal factors such as particle size, desolvation method, and history of the sample. A precise understanding of the mechanism behind such observations has been lacking up to now, and there are still substantial open questions concerning the impact of sample treatment history. The DUT-8(M) family ([M2(2,6-ndc)2(dabco)]n, 2,6-ndc = 2,6-naphthalene dicarboxylate, dabco = 1,4- diazabicyclo-[2.2.2]-octane), encompasses isostructural compounds based on Ni, Zn, Co, and Cu in the cluster node and is representative of pillared layer MOFs, often showing flexible behavior. In this contribution, we discuss a possible explanation for the differences in flexibility observed in desolvated phases of DUT-8(Cu). Theoretical calculations and crystallographic data shed light on the preferred formation of interpenetrated confined closed pore phases in DUT-8(Cu) in contrast to DUT-8(Ni, Co, Zn) where the closed pore phases are formed.