We discuss homogeneous baryonic matter in the decompactified limit of the Sakai-Sugimoto model, improving existing approximations based on flat-space instantons. We allow for an anisotropic deformation of the instantons in the holographic and spatial directions and for a density-dependent distribution of arbitrarily many instanton layers in the bulk. Within our approximation, the baryon onset turns out to be a second-order phase transition, at odds with nature, and there is no transition to quark matter at high densities, at odds with expectations from QCD. This changes when we impose certain constraints on the shape of single instantons, motivated by known features of holographic baryons in the vacuum. Then, a first-order baryon onset and chiral restoration at high density are possible, and at sufficiently large densities two instanton layers are formed dynamically. Our results are a further step towards describing realistic, strongly interacting matter over a large density regime within a single model, desirable for studies of compact stars.