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Not all system mail spools are mode 1777. Mutt needs to be setgid mail on systems that aren't, if I understand correctly. Making a python program setgid mail is a bit more of security issue than making a well-tested C program setgid, since it is easier to break out of the box in a python program.
I'm pretty sure that the shell does not parse the mbox when it produces its 'you have new mail' message. I believe it just looks at the mtime/atime.
mailbox is an mbox manipulation program, not a mail delivery agent. If you are using it to write a mail delivery agent, I think perhaps the mtime setting code belongs in your application, not the mailbox module.