My users like the SpamAssassin spam box feature. Can this be duplicated within MailScanner?

Yes, the MailScanner Front-End includes a BETA feature that is similar to the SpamAssasssin spam box. 

This enables spam email to be forwarded to a spam box for each mailbox in a cPanel account.

Go to WHM > ConfigServer MailScanner Front-End > Front-End Settings > and set "Allow users and defaults to use MSFE SpamBox (BETA)" to Yes. Click Save Changes at the bottom.

You can then either set SpamBox as the serverwide default action in WHM > ConfigServer MailScanner Front-End > Front-End Settings > "Default action for low scoring spam" and/or "Default action for high scoring spam", or allow your users to configure their own settings for spam in the cPanel Mailscanner Front-End. You can also enable the Digest Emails to send users a summary of spam received by their cPanel account. This is in WHM > ConfigServer MailScanner Front-End > Front-End Settings > "Allow users to enable Digest Emails (BETA)".