i have used model compare quite a few times, it highlights the faces that have been changed, so its not quite highlighting the differences.. so if you had a face with a hole in and in the other model the same face without, it would higlight the face and hole not just the hole.
What i find i cant do is compare two models constructed in different axis. So if two people have constructed the same model but person a has started on the xy and person b the zx plane it wont compare.