As AI systems evolve from isolated predictors into complex, heterogeneous ecosystems of foundation models and specialized adapters, distinguishing genuine behavioral novelty from functional redundancy becomes a critical governance challenge. Here, we introduce a statistical framework for auditing model uniqueness based on In-Silico Quasi-Experimental Design (ISQED). By enforcing matched interventions across models, we isolate intrinsic model identity and quantify uniqueness as the Peer-Inexpressible Residual (PIER), i.e. the component of a target's behavior strictly irreducible to any stochastic convex combination of its peers, with vanishing PIER characterizing when such a routing-based substitution becomes possible. We establish the theoretical foundations of ecosystem auditing through three key contributions. First, we prove a fundamental limitation of observational logs: uniqueness is mathematically non-identifiable without intervention control. Second, we derive a scaling law for active auditing, showing that our adaptive query protocol achieves minimax-optimal sample efficiency ($dσ^2γ^{-2}\log(Nd/δ)$). Third, we demonstrate that cooperative game-theoretic methods, such as Shapley values, fundamentally fail to detect redundancy. We implement this framework via the DISCO (Design-Integrated Synthetic Control) estimator and deploy it across diverse ecosystems, including computer vision models (ResNet/ConvNeXt/ViT), large language models (BERT/RoBERTa), and city-scale traffic forecasters. These results move trustworthy AI beyond explaining single models: they establish a principled, intervention-based science of auditing and governing heterogeneous model ecosystems.