There is not a way to change it without knowing SSH. This is set in /var/cpanel/userdata/username/maindomain.com file. If you want to change the documentroot there, you'd revise the /home/username/public_html line and then run the following commands to update Apache's configuration:
You might consider posting a feature request for the main domain to be configurable for a different path during account creation. That would be at Feature Requests for cPanel & WHM for new feature requests.
cp /usr/local/apache/conf/httpd.conf /usr/local/apache/conf/httpd.conf.bak120824