Nancey Murphy explains why Aristotelian hylomorphism successfully accounts for the perception of sensory objects, but it has more difficulty justifying perceptual errors (e.g., bent oar blades and hallucinations). On the other hand, the usual critique of atomism and nominalism is that both theories appear to imply skepticism about the world external to the mind. Rene Descartes' internalist epistemology has faced the same challenge.
While work on sensory perception is ongoing, some neuroscientists have tried to harmonize the representational view of concepts with a less skeptical view of the cosmos. One possible approach to perception is by trying to understand neural representation potentially emanating from sensory experience as a proximately identical map of the world. A second approach might entail admitting that our concepts are fuzzy, inexact "hedges" of reality. Prototype theory advocated by Eleanor Rosch seems to favor this approach.
These questions intersect with theology insofar as they impinge on theistic belief. Descartes was likely aware that his internalist philosophy entailed or implied skepticism about the external world. However, he appealed to the existence of God in order to undermine the notion that we're living a perpetual delusion of the senses.