This is a followup to a post I made to a different stream, in order to provide clarification.
We are creating custom baselines for standalone systems (Windows 7 in this case). These systems are not a part of an Active Directory infrastructure. Because SCM does not include all of the possible settings, we created custom registry.pol files that do include those settings. What we have found is that LocalGPO does not import those settings. It only appears cognizant of those settings that can be configured via the SCM. Any customized setting, such as remove "My Documents" from the desktop, prevent users from sharing files within their profile, Turn off Help Experience Improvement Program, etc., are lost when the import is performed. LocalGPO does not report an error when the import is executed.