Despite a high technical relevance and 35 years of observation, self-organized morphogenesis of nanoporous sponge-like amorphous structures during exposure of selected covalent materials to energetic ions is still insufficiently understood. Due to the presence and absence of these effects in amorphous Ge and Si, respectively, the Ge-Si alloy system constitutes an ideal testbed to track down the underlying physics at the atomic scale. This is realized within the present study by a combination of tailored experiments and extensive molecular dynamics computer modeling. The swelling capabilities of a variety of interaction potentials for the Ge-Si system and its elemental constituents are scrutinized with respect to the experimental observations and related to relevant physical properties of the model systems. This allows to identify defect kinetics in combination with a moderate radiation induced fluidity as key ingredients for nanopore morphogenesis. Cast in a simple quantitative model, it enables to account for both experimental as well as computational results, thus paving the way for a design by understanding approach in synthesis.