Hello,
Users can auto-clean their Inbox as long as it's allotted by the System Administrator. As the admin, log in and go to Settings > Storage > Folder Auto-Clean. On the Options tab, enable both settings for "Allow domains to override auto-clean settings" and "Allow users to auto-clean inbox." Now, when you change your auto-clean setting as a user, you'll have the option to select the Inbox.
Thanks!