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 allow you to tag files based on shared formatting (e.g., all scene documents look the same), rather than worrying about where they fall in the Binder hierarchy. Much more flexible than the old way.
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 Tools>Options>Backup and choose a different location for a specific project’s backup files.
All other global Backup settings (defined in Tools>Options>Backup) will still apply (e.g. file name, number of backup files retained, etc).