We recently developed a generalization of the halo model in order to describe the spatial clustering properties of each mass component in the Universe, including hot gas and stars. In this work we discuss the complementarity of the model with respect to a set of cosmological simulations including hydrodynamics of different kinds. We find that the mass fractions and density profiles measured in the simulations do not always succeed in reproducing the simulated matter power spectra, the reason being that the latter encode information from a much larger range in masses than that accessible to individually resolved structures. In other words, this halo model allows one to extract information on the growth of structures from the spatial clustering of matter, that is complementary with the information coming from the study of individual objects. We also find a number of directions for improvement of the present implementation of the model, depending on the specific application one has in mind. The most relevant one is the necessity for a scale dependence of the bias of the diffuse gas component, which will be interesting to test with future detections of the Warm-Hot Intergalactic Medium. This investigation confirms the possibility to gain information on the physics of galaxy and cluster formation by studying the clustering of mass, and our next work will consist of applying the halo model to use future high-precision cosmic shear surveys to this end.