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It seems that part of the issue is described in bug #1861881.

I was able to get a working log file while excluding the entries from syslog by:

1. removing the content from /etc/rsyslog.d/tomcat.conf (leaving blank file to prevent reinstatement by auto patching)
2. putting the content in /etc/rsyslog.d/12-tomcat9.conf (to ensure it was loaded before 50-default.conf)
3. amending the path from /var/log/tomcat9/catalina.out to /var/log/tomcat.log to avoid the permissions issue (/var/log/tomcat9 is not writeable by the syslog user)
4. adding a new /etc/logrotate.d file with content below....

/var/log/tomcat.log
{
        rotate 7
        daily
        missingok
        notifempty
        delaycompress
        compress
        postrotate
                /usr/lib/rsyslog/rsyslog-rotate
        endscript
}