Compare Features uses the feature names as the main criteria for pairing features.
If you change the name of identical features in the two parts, Compare Features classifies these features as unique. For example, the feature Hole-1 in Part A is identical to the feature Hole-1-Mod in Part B. The only difference is the name. When compared, both Hole-1 and Hole-1-Mod are classified as unique features instead of modified features.
If you have two parts with identical features, but from two different language versions of SOLIDWORKS, the features are classified as unique because their names are different.