I'm sure You have the same problem if You have a large complex folder structure. You got a new mail, but the mail rule moves it into a folder somewhere deeeeeeep....then it's hard to find. Of course You can use "copy to folder" but then your inbox will be too large. Inbox CleanUp helps...maybe, but it must be set centraly.
I think it would be an easier solution if the mail rule can - option: run after read - run after the mail is readed.