Filtering mail using the Check inboxes for new messages not sent to Mail extension and Filter spam messages in other mailboxes features is not immediate: SpamSieve needs to periodically check whether any new messages have arrived. If you receive lots of new messages and spend a lot of time in Mail, it may not be clear whether a spam message is visible because SpamSieve made a mistake and thought it was good or simply because SpamSieve hadn’t yet had a chance to examine it and move it to the Junk mailbox.
The Add green flag to unread good messages option reduces this confusion by letting you choose to mark good messages that have been checked by SpamSieve with a green flag. Messages with no flag are pending processing; they are not mistakes and do not need to be trained as spam.
Adding a green flag will make new good messages show up in the Flagged section of Mail’s sidebar, which can be useful for finding new messages that are spread across multiple mailboxes. After you read a message, SpamSieve will automatically remove the green flag, and the message will disappear from Flagged.
The Including in the inbox option works similarly but flags new good messages processed by the Mail extension. This can be useful for consistency, so that all new good messages are flagged green. You can also enable Including in the inbox but disable Add green flag to unread good messages if you are troubleshooting and want to be able to see which messages were processed by the Mail extension. There is more information about this in the Why are Apple Mail inbox messages not being processed? section.
We strongly recommend granting SpamSieve Full Disk Access. Otherwise, the green flags feature will be be slower and report an error for mailboxes containing more than 5,000 messages.