The "PPM Pro hierarchy" is a casual term that refers to the entities that comprise the PPM Pro system. Examples of PPM Pro entities include projects, issues, departments, divisions, tasks, and resources. Some of the entities have a direct relationship with other entities. For example, issues are always children of projects; tasks are always children of projects. For many years, projects were required to be children of departments, and resources were required to be children of Divisions. These latter 2 relationships are no longer required as of late 2017.
The Organization Hierarchy reflects the structure of your organization; "unit' is just a synonym for "department". The Org Hierarchy is comprised of units; units contain resource and/or other units. The Org Hierarchy is integral to the profile-based permissions model, which was rolled out in late 2017. Permissions can be granted to members of units; unit managers have certain permissions on the resources in their units.
For more information about the Org Hierarchy, see About the Organization hierarchy.