Appearance
Paper, Ink or System, plus text size and Reduce Motion. The switch in the top bar sets Paper or Ink directly; System follows macOS.
Scanning
Excluded paths, whether a scan may cross onto other volumes, whether hidden files are listed, and whether a snapshot is taken after each scan.
Cleanup
The thresholds behind easy wins — what counts as large media, and what counts as large and old — and nothing that turns off the confirmation.
The menu bar and notifications
The menu bar helper, opening at login, and whether DiskDuo tells you when a scan finishes or a disk is nearly full.