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Feature engineering remains central to materials informatics, yet systematically introduces scientific blind spots that constrain discovery and interpretation. These blind spots arise from choices in descriptor selection, transformation, and dimensionality reduction that inadvertently prioritize statistical correlations over physical invariance, overlook multi-scale interactions, and embed dataset-specific biases into model architectures. In small-data regimes common to materials science, engineered features often amplify overfitting while diminishing generalizability across chemical spaces. Interpretability suffers as complex engineered descriptors obscure mechanistic linkages between atomic structure and macroscopic properties. Literature consistently highlights these limitations across perovskites, alloys, energy materials, and porous systems, underscoring the tension between predictive performance and scientific fidelity. This conceptual manuscript synthesizes these challenges and proposes an original Integrated Blind Spot Navigation Model (IBSNM). The framework organizes feature engineering around four interdependent pillars—physical consistency guardrails, multi-scale descriptor integration, uncertainty-aware selection, and iterative co-interpretation—linked by feedback mechanisms that surface and mitigate hidden assumptions. By reframing feature engineering as a navigable landscape rather than a static preprocessing step, the model offers a conceptual pathway toward more robust, transparent materials informatics practices that do not rely on empirical validation.

The advent of computational and data-driven materials engineering has transformed materials discovery by integrating machine learning with high-throughput simulations and experimental workflows. Within this ecosystem, feature engineering emerges not merely as a technical preprocessing step but as a fundamental scientific framing mechanism that encodes domain knowledge into data representations, influencing inference pathways and discovery outcomes. This conceptual manuscript explores how encoding choices in materials informatics shape epistemic structures, steering computational pipelines from raw multimodal datasets to inverse design strategies. We identify a conceptual gap in current paradigms, where representation decisions often remain implicit, leading to unexamined trade-offs in uncertainty propagation and model interpretability. To address this, we introduce the Encoding Dynamics Framework (EDF), a systems-level architecture that conceptualizes feature engineering as an interactive layer between data infrastructures and AI-guided discovery systems. EDF highlights feedback loops where encoding selections modulate representation learning, graph neural networks, and closed-loop experimentation, fostering more robust computational steering logics. Implications extend to foundation models for materials science, simulation-experiment coupling, and uncertainty quantification, promoting infrastructures that align encoding with scientific inquiry goals. By reframing feature engineering as epistemic framing, this work advances interpretive insights into how data encoding choices drive materials innovation without empirical validation.