Solved!!
The problem was not in the definition of the virtual hosts, neither in the duplication of the domain name due to the default server. The problem was in the apache2.conf file, the include line for the vhosts at the very end of the file was:
Include /etc/apache2/sites-enabled/[^.#]*
I don’t why it had such strange wildcards at the end, but when I changed it to
Include /etc/apache2/sites-enabled/*.conf
certbot-auto was able to show the list of enabled domains and the challenge finished correctly. I hope this info will be useful for other people.
Thank you for your help.