The rc scripts for the beats promise to respect for example the filebeat_conf variable, yet the script itself doesn't. Reproduce by setting filebeat_conf="/root/filebeat.yml" while removing /usr/local/etc/filebeat.yml from the system. Upon starting filebeat using /usr/local/etc/rc.d/filebeat start, a lot of noise will come your way about filebeat not being able to find /usr/local/etc/filebeat.yml.