Hi,
Please let me know what configuration you would want to ignore.
The Centralized configuration will overwrite the agent's configuration in case they are conflicting with each other.
So it is possible to use agent.conf to overwrite default agent's configuration that you do not need. For example, for FIM you can set the <ignore> tag. There are some configurations (like Vulnerability Detection) can be disabled/enabled with the specific tag. For Log Collection you can "break" the monitoring by setting the wrong <log_format> (for example instead of syslog - you change it to json, and vice versa).
Please let me know if you have any questions.
Best regards,
Bin.