It's often relevant if you get an error message where the CA tried to validate the domain and failed—we can often do tests and see if there is a DNS misconfiguration. In some cases we wasted a pretty large amount of time with problems that experts on this forum could have identified in a matter of seconds if we had seen the domain names, such as a DNS error that we had seen in other cases.
However, I agree that in this case the error does not appear to be one that we could diagnose by seeing the domain name.
In this case, the "note: conf files with multiple vhosts are not yet supported" is probably an important clue. This means that your version of Certbot doesn't know how to deal with an Apache configuration file that contains more than one virtual host definition in the same file (as opposed to the commonly-suggested approach of making a separate file in /etc/apache2/sites-available for each virtual host). This is apparently the case with the configuration files that you posted above... it looks like you're just adding more virtual hosts to 000-default.conf instead of making new, separate Apache configuration files when you add each virtual host. So that might be confusing your Certbot when you try to get certificates that relate to the names supported by your various virtual hosts.