What i mean is that certbot first looks in the directory /var/www in that sample script, finds a site and then add every site in that directory to the first cert. /var/www/ is the main site and var/www/vdomain1 is next with /var/www/vdomain2 being the third that is wrapped into the cert. in my case they are all under /home/vdomain1/public_html /home/vdomian2/public_html
etc with no domain residing at the root /home directory…