To create and apply a customized security template I did the following:
Use a template based in Security Compliance Manager
Deploy a temporal standalone WS 2012 R2 to do tests
Import the .inf file exported from GPO Backup (folder) option in SCM to a Security Template mmc and then modify all options you want.
Add Security Configuration and Analysis snapin, import your template .inf and then execute the analyze option, remember to use a new database.
Save configurations as inf file and it will be your security template for hardening.