I think it's equally important to remember that how programs react to values in the registry is part of that program's behavior, not part of the Administrative Template policy functionality.
Each GPO containing Administrative Templates is 'overlaid' on the registry during Group Policy processing, and any values specified in that GPO overwrite values previously loaded there (either because those values were in the registry by default, or because they were put there by a person or another GPO). Personally, I think that thinking about Administrative Template policies like registry manipulation seems more intuitive. Group Policy Administrative Template policies don't do anything more than set registry values (typically under Software\Policies in HKEY_CURRENT_USER and HKEY_LOCAL_MACHINE, as well as a couple other locations, or anywhere that a third-party ADM(X) file might want to set them).
