Q1 2020 Agari Phishing Defense released "Processing Exceptions" which allow you to have more control over what messages are processed and which are not. This is a very powerful functionality and should be used with care.
Under Manage > Organizations > Processing Exceptions you will see a number of changes you can make. The first setting is the Spam Confidence Level (SCL) score. Spam scores of 5 and above are considered spam by Agari. By default, these (or exempts) messages are skipped so that Agari does not learn patterns from messages already deemed as spam. This can be changed as needed but should be used with caution.
The next setting allows you to customize messages you want to be exempted from all Agari scoring. The common use case here is for messages sent internally and intentionally to your SOC team for analysis where known malicious content will be included. Again, this is incredibly powerful as none of these messages will be processed by Agari and will bypass any policies you have.