The man at the college who used GIMP software was certainly well-meaning, but he was also a complete, total amateur and without much common sense. He didn't even know how to use photo software.
When taking his own photo, he didn't look at the camera but his face on the screen, which changes the angle of the head. But this is what a rank amateur does when they use a web cam. Then, rather than taking a photo of the plastic skull at the same angle as his photo, he takes it straight on, and then he tries to match the two angles. This was really stupid. When comparing the photo of the girl with the photo of the skull, he did not rotate the photo first. If he had he would have been able to notice if there were any issues with symmetry (with many people is a slight, almost unnoticeable lack of symmetry - one ear a little lower, a slight skewing of the mouth, etc.). Rotating the image to being level is always the first step. The business of matching the angled photo was really stupid.
Luckily, things worked out. Chances are that there would have been several dozen photoshop users who would have done a better job and much faster. Having an IT guy - a fellow who chases bugs in Windows PCs and manages a server - was a stupid choice by the forensic anthropologist. Just because someone fixes computers, this does not make them an expert in photographic software.
Again, they were lucky.