There are a few methods on WebPreferences that toggle globals (e.g. AVFoundationEnabled, ShouldPaintNativeControls, MockScrollbarsEnabled, ShouldUseHighResolutionTimers). These would be better as WebView class methods.
WebPreferences is the thing that syncs with on-disk defaults, so they are all global. Am I confused?
Standard WebPreferences are persistent by default. A WebView’s preferences can be the standard preferences or any other WebPreferences instance, which may or may not be persistent. The methods mentioned in the Description, however, take effect on all WebViews in the process, regardless of their preferences, and regardless of the WebPreference instance on which those methods are invoked.