We mention OS packages as an option to install Certbot at https://github.com/certbot/certbot/blob/master/certbot/docs/install.rst#operating-system-packages. Potential problems with using these packages include they're old (so your generated TLS config is worse, Certbot has more bugs and less features, etc.), not all plugins are available, or they do not preconfigure certificate renewal.

I think we should add a note to the top of this section to flag this for people.