MariaDB upgrade fails in postinst (DEB)

mariadb-server-10.0 package was failing with exit code 7.
After trying to track down the exact cause using a number of manual debug techniques we found the error was happening when running "/bin/bash /usr/bin/mysql_install_db --rpm --user=mysql --disable-log-bin" in the postinst script. This was because variables in the my.cnf file were not recognised.

The following varliables needed to be commented out for it to run:

query_response_time_stats=ON
server_audit_output_type=syslog
server_audit_logging=ON
server_audit_events=QUERY_DDL

Uncommenting them after the upgrade seems to be causing no issues.