When creating site with koha-create with a third level domain the ServerName directive in the /etc/apache2/sites-enabled conf file doesn't put a dot between library name and domain name. Both for OPAC and Intranet sections. Therefore you are unable to reach both the interfaces, public and staff.
You likely edited out the initial . from the DOMAIN in the /etc/koha/koha-sites.conf file before you did your koha-create command. If you place the initial . in the DOMAIN variable, it doesn't matter how many levels of domains are being used. Around line 589 in /usr/sbin/koha-create: opacdomain="$OPACPREFIX$name$OPACSUFFIX$DOMAIN" intradomain="$INTRAPREFIX$name$INTRASUFFIX$DOMAIN"