Yes, that's a big subject bothering me from the start
The issue is that the Library contains Thea and Maxwell files that contain hardcoded paths to textures. These paths are not accessible by Skatter itself, so they can't be dynamically changed.
So I made the choice to enforce the location of the files so that it works out of the box, otherwise people using these files would have to change the paths every time they update Skatter.
But I'm open to better solutions!