What is the difference between these folders in the ~/Library/Application Support/Scrivener/ folder, and which should I choose for the shared templates folder in the Preferences?
I believe the first is where Scrivener stores Project Templates, which are just projects that are transformed into templates using the File->Save as Template on, presumably after you clear out any text/settings that are specific to a given writing project.
The shared Document Templates folder that you set is for having a central location for documents that multiple projects can use as a source for starting new documents in the binder. They’re just a global version of the per-project document templates folders that you can also set in the Project settings window.