I'm noticing that RMM doesn't take into account the automatic unsubscribe click that iOS offers when an email is part of a 'Mailing List'.
OK I think the disconnect is that the emails generated from the iOS auto-unsubscribe link are not actually replies. (Some good information on the iOS auto-unsubscribe link - info only on #1)
The destinations (mailto and URL) to send the auto-unsubscribe is set inside the email header using list-unsubscribe. The setup for this is handled by SFMC. You would likely need to talk with Global Support or your rep to have them customize these settings for you to make it easier to automate.
I would highly recommend this as list-unsubscribe is used in quite a few of the web-based email clients, including Gmail and most Google clients. The difference is that Apple only accepts the mailto: link and not the URL, meaning all clicks on that are going to the email address listed in the header.