The content in:

/usr/local/etc/routinator/routinator.conf.system-service

suggests that the tal directory should go to:
tal-dir = "/var/lib/routinator/tals"

but after renaming 
/usr/local/etc/routinator/routinator.conf.system-service
to
/usr/local/etc/routinator/routinator.conf

and preparing the tals directory, routinator refuses to start with the following message:
Need to initialize routinator with tals, see man routinator

This is because the rc.d script ignores what the config says and checks another directory: /var/routinator/tals


[...]
: ${wrkdir:="/var/routinator"}

pidfile=${wrkdir}/${name}.pid
routinator_config=${routinator_conf:-"/usr/local/etc/routinator/routinator.conf"}
required_file=${routinator_config}
command_args="-c ${routinator_config} --rsync-command=/usr/local/bin/rsync server -d --user routinator --group routinator --pid-file=${pidfile} --working-dir=${wrkdir}"

check_init() {
	if [ ! -d ${wrkdir}/tals ]; then
		echo
		echo -n "Need to initialize routinator with tals, "
		echo "see man routinator"
		echo
		exit 1
	fi
}



So I suggest to change the sample config paths for consistency:
repository-dir = "/var/routinator/rpki-cache"
tal-dir = "/var/routinator/tals"