Predictive uncertainty is commonly decomposed into epistemic and aleatoric components, but standard decompositions often produce strongly correlated estimates because both quantities are derived from the same predictive distribution. We study an alternative design principle, \emph{structural separation}, which assigns epistemic and aleatoric uncertainty to disjoint parameter paths trained with distinct supervision targets: reducible prediction error for epistemic uncertainty and persistent label ambiguity for aleatoric uncertainty. We instantiate this principle in two supervised latent-variable models, a Credal Concept Bottleneck Model and a credal Self-Explaining Neural Network, and prove a gradient-isolation result showing that the two uncertainty heads are not coupled through shared training gradients under the proposed parameterization. Across five ambiguity-aware benchmarks, structural separation substantially reduces epistemic-aleatoric correlation while preserving predictive performance. Further analyses show that aleatoric estimates track annotator- or corpus-derived ambiguity, while epistemic estimates are more sensitive to prediction error and data availability. These results suggest that supervised latent-variable architectures provide a practical route toward uncertainty estimates that are not merely decorrelated, but operationally distinguishable.

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