Yes, reports can be generated from command line. You should pass two parameters to "TopReports.exe" executable - first parameter is a path to Outlook folder (e.g. "\\Outlook\Inbox") and second a file name where to save the report to (e.g. "C:\Inbox report.tro").
We recommend specifying file extension as *.tro, the reports then can automatically be open with Topalt Reports.