I think settings and preferences should be synonyms.
"Settings" is a more general term that applies to driver settings, program settings, system settings, etc. "Preferences" is a term that usually refers to program settings; for example, the GUIs of most programs in Ubuntu call the program's settings "preferences". Nonetheless, many people still call those "settings" rather than "preferences". So if we want separate tags based on this distinction, they would need to have more descriptive names like system-settings.
Since "preferences" is a subset of "settings", I think preferences should be a synonym of settings.