MacOS – My Mail app (MacOS Catalina 10.15.3) displays phantom unread messages

For some reason or another, Apple has made it impossible to access junk messages from a Smart Mailbox.

If you are able to set Message is in Mailbox to Junk, you must be setting it to a special 'Junk' mailbox that you have created (or that was created automatically by whatever email service you connect to). So, messages in Mail's built-in Junk folder won't appear in your mailbox.

However, you can get around this without too much trouble. To do this, make a Mail rule that automatically moves junk mail to your special Junk mailbox. Here's how:
Go to Mail-> Preferences-> Rules. Click Add Rule. Set the description to something like Move to special Junk. Set the popup in the first box to Message is Junk Mail. Set the first popup in the second box to Move message, and use the second popup to select your special junk box.

Now, any incoming messages that Mail thinks are junk will go to your special junk mailbox. You can use this one in a Smart Mailbox.

Hope this helps!

It seems Mail 6.0 in Mountain Lion has fixed this for me. When I have new mail it shows as unread in both my in-box and my archive mailbox. And now, when I read it in my in-box it gets marked as read in both my in-box and my archive mailbox. Chalk one up for Mountain Lion.