Comparing internal representations is a central goal in neuroscience and machine learning, but standard linear alignment metrics (Representational Similarity Analysis, Centered Kernel Alignment, and linear regression) are frequently applied to neural activity coordinates rather than on the underlying features. We show this matters when neural systems operate in superposition, encoding more features than they have neurons via linear compression. Closed-form derivations prove that these metrics depend on the Gram matrices of each system's projection, not on the latent features themselves: alignment thus combines what a system represents with how it is encoded. For those interested in what features two systems share, this is a problem: Two networks can have identical feature content yet appear more dissimilar than networks exhibiting partial feature overlap. This apparent misalignment need not reflect lost information as compressed sensing guarantees sparse features remain recoverable from the compressed activity. We confirm this by training supervised TopK sparse autoencoders that realize solvable compressed sensing by construction, finding alignment on recovered latents restored even when raw-activation alignment remains deflated. We extend the result to unsupervised SAEs trained without ground-truth latents, and to pretrained vision and language model SAEs, where SAE-latent alignment exceeds raw-activation alignment, consistent with superposition in real systems.

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