/etc/httpd/conf/httpd.conf is the Apache configuration file that Apache actually reads.
Inside that /etc/httpd/conf/httpd.conf file is a series of Include files, one of which is:
/etc/httpd/conf/extra/directadmin-vhosts.conf
When you create a new user, an httpd.conf file is created at /usr/local/directadmin/data/users/%user%/httpd.conf AND an include line is added to /etc/httpd/conf/extra/directadmin-vhosts.conf which includes this /usr/local/directadmin/data/users/%user%/httpd.conf file.
This /usr/local/directadmin/data/users/%user%/httpd.conf file contains all of the VirtualHost entries for the domains associated with %user%,
So when Apache is reloaded:
It reads /etc/httpd/conf/httpd.conf which leads to reading /etc/httpd/conf/extra/directadmin-vhosts.conf which leads to reading /usr/local/directadmin/data/users/%user%/httpd.conf
That is how VirtualHost entries get read by Apache.