MacOS Mail app rules to delete are archiving instead

It turns out that the solution was to log into icloud.com, find all the emails that keep being marked as junk (since they will actually appear as junk in icloud) and mark them as not junk. Now mail.app correctly treats them as not junk and is no longer sending them (marked as not junk) to the junk folder.

One solution could be as follows:

1. In Macbook, create an Apple script that uploads new emails and marks emails in a given folder as read:

   tell application "Mail"
   check for new mail
   set read status of messages of mailbox "Deleted Items" of account "XXX" to true
   end tell
   

Note that emails that are deleted on iphone do not end up in the Trash but Deleted Items folder in the Mail app on Macbook.

2. Using the inbuilt Automator on Macbook, create and store an .app that executes the above script.

3. Use freeware ControlPlane to run the above app upon each log-in. I allowed for a time lag of 10 seconds for the Macbook to establish Internet connection before the app is executed.