Project settings are those that apply only to the project you're working on. There are two big ones that have been added in Scrivener 3.
Section Types are a new way to define the formatting of documents and folders during the compile process. Under Project>Project Settings>Section Types, you can define section types specific to the current project (not global to all projects). These will change the compile process significantly, hopefully for the better. 😉
I’m really excited about this one. In the previous version of Scrivener, all files included in Automatic Backups were backed up to the same location. Now, under Project>Project Settings>Backup, you can override the location specified for all projects under Scrivener>Preferences>Backup and choose a different location for a specific project’s backup files.
All other global Backup settings (defined in Scrivener>Preferences>Backup) will still apply (e.g. file name, number of backup files retained, etc).