This feature appears to currently only be available in Virtualmin Pro. I suspect that’ll change in a couple of revisions (as it’s not a feature that requires a huge amount of maintenance or ongoing development).
I think the fact that the functions of “Automatically delete spam?” and “Automatically delete trash?” in “Server Configuration=>>Spam and Virus Delivery” are not working is related to “Mailbox Cleanup” new feature, I say that because it was working before 4.11 release.