I'm experiencing the same issue after updating to v58 and/or EA4 as well (not sure what caused it). The LogFormat change from %h to %a will not stick anymore - it was working fine before that.
Even after using /usr/local/cpanel/bin/apache_conf_distiller --update and regardless of whether I edit /var/cpanel/conf/apache/main or /usr/local/apache/conf/httpd.conf, as soon as I run /scripts/rebuildhttpdconf %a is changed back to %h and my logs start showing Varnish's IP again.
Even after using /usr/local/cpanel/bin/apache_conf_distiller --update and regardless of whether I edit /var/cpanel/conf/apache/main or /usr/local/apache/conf/httpd.conf, as soon as I run /scripts/rebuildhttpdconf %a is changed back to %h and my logs start showing Varnish's IP again.