RSA and CKA are standard metrics for comparing neural representations across brain regions, organisms, and deep learning models. We demonstrate a fundamental weakness: these decoding-based metrics are insensitive to encoding manifold topology—the internal functional organization of a neural population. In a controlled MNIST experiment, RSA, CKA, and Procrustes R² remain statistically unchanged when encoding topology is causally manipulated via an auxiliary clustering loss, while the two model populations differ significantly in attribution patterns, weight-graph assortativity, and out-of-distribution robustness. Across biological systems and machine learning models, similar decoding behavior can arise from small, non-representative subpopulations, and alignment metrics are insensitive to encoding manifold topology even when it is fundamentally altered. These findings bear directly on mechanistic interpretability: standard alignment metrics cannot distinguish whether two networks share the same computational circuits or merely produce indistinguishable aggregate outputs. We propose encoding manifolds and Gromov-Wasserstein distance as complementary diagnostics for any decoding-based similarity claim, and provide a Neural Manifold Explorer tool at https://johannesbertram.github.io/FNN_Manifolds/index.html for further experimentation.