To run TreeSize under a different user account, you can either start the application using the 'Run as' command which is available if you [Shift]+[Right-Click] the executable, or you can create a scheduled task.
For the 'Run as' command you will have to enter the credentials each time the application shall be executed for that specific user, while for the scheduled task entering the credentials is only required once.
Yes, TreeSize can report on the directory level. You can view thedir level for any folder or file in the 'Details' view. To activate the column, right click on the column header of the details view and choose the appropriate column. The absolute dir level is counted from the root of the drive, the relative dir level from the path where you started the scan.
If you need to filter a scan result for a specific directory or file level, you can use the Excel export from TreeSize. After scanning the system you can now use the 'File > Export > Excel File' button to create an Excel file that contains the scan data. With the filter features of Excel, you can now filter for any criteria.