As part of learning the newly-installed trial version of SpamSieve 3.0.2 (e.g. it moves a message to the Junk folder when I ‘train as spam’), I realized that I don’t understand mail.app’s default behavior! What happens when I click the mail.app ‘Junk’ button (for a message from a POP account)? Is the email gone forever? Hidden somewhere?
(I realize this isn’t directly a SpamSieve question. No luck finding an answer via a Web search or ChatGPT so I’m trying this forum.)
Apple Mail’s Junk toolbar button should not be used with SpamSieve because that trains Mail’s filter. You should instead use the Train as Spam menu command. But, to answer your question, the Junk button will move the message to the special Junk mailbox for its account.
Thanks! These Junk folders will be useful for ‘Train as Spam’ – especially since (based on a quick test) that does NOT move them to the shared/global Junk folder.
I didn’t know such things existed – I never scroll down the far. (In case useful to others: in the left sidebar, scroll to the bottom and expand the disclosure triangle behind any account. Some have their own Junk folder; others don’t.)
Apple Mail does not have a shared/global Junk folder. If you see such a mailbox without the special junk icon, that’s just a regular mailbox that perhaps you created yourself. It would not be used by SpamSieve or by Mail’s own junk filter.
What Mail does have is an optional special mailbox under Favorites called All Junk. This is essentially a smart mailbox that shows the contents of all the per-account Junk mailboxes together, at the top of the mailbox list, so that you don’t have to dig into them individually.
Mail.app 16.0 on macOS 12.7.1 Monterey.
In the mail.app sidebar, the first entry under ‘On My Mac’ is Junk with the ‘x’ icon. (Then Trash then Archive.) It doesn’t seem to be tied to any other account – though of course I could be missing something. 
Scrolling down past my many folders, there’s a separate section for each of my accounts. Most contain Inbox, Drafts, Sent, Junk, Trash.
There’s no overlap between the messages in the top Junk folder and the others.
That might be the account-specific mailbox for a POP account.