Though this Report has a Column that shows the number of individuals contained in one of your Departments ('Users') - as well as a Column that shows the number of individuals that are in that same Department plus all of the people contained in any of its related Sub-Departments ('Users (including Sub-Depts)'), the three performance statistics provided in this Report (i.e. Average Score, Progress and Progress of Enrolled Columns) are only calculated using the numbers from the first column, the top level 'Users' Column.
Why do the performance statistics only reflect data from the Users and not the Users plus sub departments?
This is because a Department in Absorb can potentially have a large number of Sub-Departments (with each of those also possibly having any number of Sub-Departments of their own as well) and it would confusing to have more than one Department's stats on the same row - especially if you wanted to look at the same three Columns for each member that is part of a particular departmental hierarchy. Therefore, the the Report only has performance data listed for one Department and one level at a time.
If you want to get a combined performance stat for an individual Department including all of its Sub-Departments, you will need to gather the separate values of that particular Column from each of the applicable Department rows in your Report, and then average them together.