How are you starting metricbeat with systemctl / systemd
Did you see this?
When Filebeat is running on a Linux system with systemd, it uses by default the
-ecommand line option, that makes it write all the logging output to stderr so it can be captured by journald. Other outputs are disabled. See Filebeat and systemd to know more and learn how to change this.
I think you just need to follow the example and create a log.conf that looks like this (I think this gets rid the -e but I don't have a filebeat installed on linux with a package handy... but this should point you in the right direction, then I think it will honor your logging settings.
[Service]
Environment="BEAT_LOG_OPTS=