The main difference is that I don't own the subdomain, and should the organization decide to forgo the domain, my subdomain is also gone. On the other hand, if I buy a domain, my name is attached to it in the registry to denote that I am the "rightful" owner of the domain, and it is going to be way harder for me to lose access to it (I read a post on HN sometimes ago that some governmental cybersec task force can just terminate access to your domain if they deem you are using it for malicious intent, but otherwise you can only deliberately lose the domain)
This is just like a github.io subdomain. IME the only true free domain service is Freenom.