Yes, because an object's transform (position, rotation, and scale) is independent of its mesh data. So you can duplicate the cube, scale it and rotate it, and the mesh data underneath both cubes would still be considered equal.

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.