Preferences currently only relate to registration information and Tinderbox versions.
The old Preferences have now become Document Settings, applying only to the current document. Many Document settings act as default values for System attributes. Whilst a few System attributes are calculated on the fly and thus read-only, all other attributes can be manually set a doc-level default.
Preferences have been significantly revised and reduced from pre-v6 designs.
See also—notes linking to here: