Would it be possible to get an FTP daemon to be configured on startup of the Let’s Encrypt container? That could be used to manage files within the /config folder. I currently have a couple of websites hosted on my instance and the only way to edit files is to use WinSCP to access the CentOS server it is running on and go through the Docker volume I have created for the container, which I have heard is a bad idea apparently.
The FTP daemon could be configured to use the certificate generated by cert-bot as a way to enable SFTP/FTPS support. The certificates issued always have the Server Authentication property which means they can be used for not just HTTPS but any server that needs to encrypt traffic.