Yes. In addition to the fact that Group Policy Preferences offers a GUI interface to create the Preference settings, there is a key difference in how both of them are enforced. Settings created by Group Policy are enforced so that if desired, the user cannot reverse the settings. Group Policy can completely disable certain operating system and application features while Group Policy Preferences cannot.
The very word Preferences infers that these are simply suggested baseline settings. The user can alter these settings if desired; however, the configured settings are refreshed at the normal Group Policy interval. In addition, settings are not removed once the GPO falls out of scope.