Scientific theories provide extraordinarily successful descriptions and predictions of the physical world, yet their epistemic success does not by itself determine the ontological status of the entities, structures, and concepts found in those theories. This paper examines the distinction between epistemology and ontology through the broader philosophical tension between scientific realism and instrumentalism. It argues that a successful scientific representation should neither be regarded as merely a convenient computational instrument nor automatically identified with reality itself. Rather, scientific knowledge occupies an intermediate domain in which conceptual and mathematical structures provide access to an objective reality while simultaneously imposing conditions on how that reality can be represented and understood. The distinction between form and content provides a framework for examining this relationship. Mathematical form may possess extraordinary predictive and explanatory power without settling the question of what, ontologically, constitutes the physical content represented by that form. The analysis presented in this paper differentiates epistemic limitations from ontological indeterminacy, mathematical determinism from metaphysical determinism, and conceptual descriptions from the realities they seek to represent. Moreover, we can state that scientific theories can provide genuine knowledge of objective structures in reality while remaining epistemically limited representations rather than transparent descriptions of reality in itself. Recognizing this distinction does not weaken science; rather, it establishes a more careful boundary between what a theory demonstrates, what it represents, and what may legitimately be inferred about the ultimate nature of reality.