Securing phpmyadmin with LetsEncrypt SSL?

This old article on securing phpmyadmin with SSL still does the trick on Ubuntu 14.04 LTS and above.

However, the method in the article has two problems I would like to avoid:

1. On first access to the SSL protected phpmyadmin url, it throws an SSL warning due to the self-generated cert
2. 000-default.conf is modified to listen to Port 443 rather than Port 80, so loading the IP address of a droplet redirects to the home page of the first web site hosted on the server (if multiple sites are hosted) or to the only only web site hosted on the server, as the case may be.

I would like to resolve these issues by finding a way to use a LetsEncrypt cert rather than a self-generated one for the phpmyadmin url. I know that LetsEncrypt certs are tied to Apache virtual hosts, but it’s not clear to me which is the domain for which I should get a LetsEncrypt cert to have an SSL protected phpmyadmin url.

I suppose I could create a vhost for the FQDN of the server and then try to get a LetsEncrypt SSL for that fqdn. But it’s not clear to me what is the document root to specify for phpmyadmin within the vhost. Nor is it clear to me what the alias address should be modified to at /etc/phpmyadmin/apache.conf to work with this setup.

Does anyone here have any suggestions?