All your examples are describing various aspects of the space itself, i.e. all objects that you listed are just different collections of points/records/objects.

All your examples are describing various aspects of the space itself, i.e. all objects that you listed are just different collections of points/records/objects. A hierarchy, or a graph in general, is different in that, in addition to describing a set of nodes/objects/records/points, it additionally describes relationships among these things. So a hierarchy (graph) is two sets: points (objects/etc), and edges (relationships) among the points.