@Matt Venn One other technique that I have seen being used is the existence of some form check condition specially for security related digital circuitry. I wasn't involved on that side of checks. They make sure to insert some extra digital circuitry in critical areas connected to the output to make sure that hardware has not been altered. But for Mask review, I have done that many many times and it was done for both security and quality related measures. We sent the GDS and get the Mask files back from the foundry and compared it against our in house mask evaluation. Each Mask layer should have a known derivation from the drawn layer and it's documented in the DRM (Design Rule Manual).