I don't see support listed for APFS volumes, yet.
"The latest version of SuperDuper! is faster, better, compatible with macOS High Sierra HFS+ volumes - in fact, it's compatible with macOS 10.8 and later), and improves many parts of the user experience."
Carbon Copy Cloner is. It comes with a 30 day trial. You could use that to backup the APFS drive, until SD had support.