Mail message delete preferences don't work and all the messages about this are 12 years old. I have to delete messages manually from both my junk and trash folders.

See these articles https://support.postbox-inc.com/hc/en-us/articles/202200580-Delete-Behavior-for- Gmail-Accounts

How does Gmail POP work? - G Suite Administrator Help

See this apple article Mail Mailbox Behaviors preferences on Mac - Apple Support

In the screen shot check the boxes shown with arrow and scroll down in the window and click on save , this is an example for Gmail pop account .

Might be a corrupt .plist.

Do a backup, preferably 2 backups on 2 separate drives.

Quit the application.

Go to Finder and select your user/home folder. With that Finder window as the front window, either select Finder/View/Show View options or go command - J. When the View options opens, check ’Show Library Folder’. That should make your user library folder visible in your user/home folder. Select Library. Then go to Preferences/com.apple.mail.plist. Move the .plist to your desktop.

Restart the computer, open the application, and test. If it works okay, delete the plist from the desktop.

If the application is the same, return the .plist to where you got it from, overwriting the newer one.

Thanks to leonie for some information contained in this.

It depends upon the internet service provider , how to treat / delete the mails from their server end , the time limits have been set by them , however you do the settings at specified time to delete the mails in the IMAP account .