Hey Christopher,

 

I believe you'll need to set the folder auto-clean rule on a per user basis for any of the non-default folders.  The specific user will have to login and navigate to filtering, folder auto-clean, and override the settings for their account.  From there they should be able to select their specific folders and apply the auto-clean rule.  I don't believe you can do this at the domain level.

 

Hope this helps.