When you modify a setting that’s under “Administrative Templates” in the group policy editor, it gets stored in a file called registry.pol in the GPO’s folder. Assigning those settings directly in the registry has a similar effect as far as the system’s behavior is concerned, but you won’t see the changes in the Group Policy console.
There’s no built-in way to modify these registry.pol files from a script or command line in a local GPO, but I wrote some C# code to work with them a while back: http://gallery.technet.microsoft.com/scriptcenter/Read-or-modify-Registrypol-778fed6e . (Fair warning: it’s kind of ugly, but it works. I didn’t have much experience with C# or PowerShell when I wrote it.)