MnBi$_{2}$Te$_{4}/$(Bi$_{2}$Te$_{3}$)$_{n}$ materials system has recently generated strong interest as a natural platform for realization of the quantum anomalous Hall (QAH) state. The system is magnetically much better ordered than substitutionally doped materials, however, the detrimental effects of certain disorders are becoming increasingly acknowledged. Here, from compiling structural, compositional, and magnetic metrics of disorder in ferromagnetic MnBi$_{2}$Te$_{4}/$(Bi$_{2}$Te$_{3}$)$_{n}$ it is found that migration of Mn between MnBi$_{2}$T$e_{4}$ septuple layers (SLs) and otherwise non-magnetic Bi$_{2}$Te$_{3}$ quintuple layers (QLs) has systemic consequences - it induces ferromagnetic coupling of Mn-depleted SLs with Mn-doped QLs, seen in ferromagnetic resonance as an acoustic and optical resonance mode of the two coupled spin subsystems. Even for a large SL separation (n $gtrsim$ 4 QLs) the structure cannot be considered as a stack of uncoupled two-dimensional layers. Angle-resolved photoemission spectroscopy and density functional theory studies show that Mn disorder within an SL causes delocalization of electron wavefunctions and a change of the surface bandstructure as compared to the ideal MnBi$_{2}$Te$_{4}/$(Bi$_{2}$Te$_{3}$)$_{n}$. These findings highlight the critical importance of inter- and intra-SL disorder towards achieving new QAH platforms as well as exploring novel axion physics in intrinsic topological magnets.