What is the point of having thigns actually be just files in the filesystem if it's just a mess of things piled up in the same place? If there is a whole layer of software making that mess not be a mess, then whats the point of using the file system ?
The point is having things be organized, if there is need to always know where somthing is, don't hardcode a path, use a way that no matter where the things is, you know it (like an environment variable, or identifying the path for the thing somewhere, be it a registry, or a filesystem abstraction like symlinks that always have the same name, under a folder that is always the same etc). Hardcoding values that people might have some reason (even reasons you can't think off) to want to change, is a bad habit.