By default, the file container-executor.cfg under /etc/hadoop/conf/ is overwritten in every nodemanager by /var/lib/ambari-agent/cache/common-services/YARN/18.104.22.168.0/package/templates/container-executor.cfg.j2
When you have LinuxContainerExecutor , yarn execute jobs as the end user, in this case It's not recommended to change banned.users and allowed.system.user
Why you should ban super user from running Yarn jobs ? this is because anyone can run the job as "super-user" within hadoop group , hadoop trust what user you say you are when submitting jobs - if you pass kerberos wall with the keytab.( which can easily be found and used in the job ) - then any user can basically have full super user permissions on job submission.