This workflow will allow you to bake in protections for families that aren't part of your template.
Create a new project or sandbox file that you can batch load your families into. Apply protections to those families in the Guardian Mirror Protection and Protected Families dialogs.
Locate the families you selected in the Protected Families dialog in the Project Browser and right click + save them back to your library. Those families will now have Guardian level protection baked into them!
Reach out to learn more, ask any questions, or meet the team! We'd love to learn more about your challenges and explore the more proactive solution.