The algorithms comparing meshes are not 100% comprehensive. The native method is sometimes too exact with how Blender manages mesh attributes, leading to false negatives where identical meshes are not 100% the same in Blender's eyes. The hash method is more approximate, which can lead to false positives. While I do what I can to improve the accuracy of these algorithms, there will likely be inconsistencies. If you need further precision, do a manual inspection of the mesh.