I wonder if perhaps you have misunderstood what "private" means in the context of FreeDNS:
2). Shared: Private - If you add your domain as private, this is the area you will screen your domains of which you decide to keep, or deny. While domains are in the queue they will function . By choosing this, you agree to only deny those that you deem offensive, or slanderous.
So, this allows other people to create subdomains of your domain, which in turn allows them to create certificates for those subdomains.