The mathematical modeling of multicellular systems is an important branch of biophysics, which focuses on how the system properties emerge from the elementary interaction between the constituent elements. Recently, mathematical structures have been proposed within the thermostatted kinetic theory for the modeling of complex living systems and have been profitably employed for the modeling of various complex biological systems at the cellular scale. This paper deals with a class of generalized thermostatted kinetic theory frameworks that can stand in as background paradigms for the derivation of specific models in biophysics. Specifically, the fundamental homogeneous thermostatted kinetic theory structures of the recent literature are recovered and generalized in order to take into consideration further phenomena in biology. The generalizations concern the conservative, the nonconservative, and the mutative interactions between the inner system and the outer environment. In order to sustain the strength of the new structures, some specific models of the literature are reset into the style of the new frameworks of the thermostatted kinetic theory. The selected models deal with breast cancer, genetic mutations, immune system response, and skin fibrosis. Future research directions from the theoretical and modeling viewpoints are discussed in the whole paper and are mainly devoted to the well-posedness in the Hadamard sense of the related initial boundary value problems, to the spatial–velocity dynamics and to the derivation of macroscopic-scale dynamics.