The nominal links /etc --> /private/etc, /tmp --> /private/tmp and /var --> /private/var are all straightforward and I understand they are there because of a legacy need that has passed. Nothing magical about them.
However, I just saw these install instructions for an Apache/httpd module which recommend using /private/libexec instead of /usr/libexec. That directory doesn't exist but I can create it via sudo. So, I am wondering if /private has some special properties such that /private/libexec is merged with /usr/libexec?