And the same goes for the hostnames, as they only exist in your hosts file, right?
In that case you can't use a Let's Encrypt certificate for those specific hostnames, as the Let's Encrypt validation server needs to be able to validate the hostname, either by connecting to its IP address or by resolving a special TXT resource records on the DNS zone.
You could however use wild card certificates. I.e., get a certificate for *.domain1, *.domain2 et cetera. This would however require the use of the dns-01 challenge, which could be harder to set up compared to the http-01 challenge. Another reason to switch to the CentOS package manager to install certbot: it's relatively hard to install one of the DNS plugins while using certbot-auto.