It is flat out wrong to have parent_id set to -100, one of several things that needs fixing in file storage. It means that mounting file storage under a subsite results in permission inherited from node -100, which makes more sense.
This has been on my personal hit list of things to fix but I didn't get to it for 5.0.
.LRN renames folders for file storage to names related to the class or community.
Setting parent_id to NULL isn't right either but maybe is necessary given the fact that the parent_id is assumed to be a folder ...