This makes sense to me too.
I would like to turn email replies off for the site in order to encourage engagement on our actual site (with all the benefits of user tracking, richer experience, higher quality posts, no email gumpf or unwanted attachments etc etc).
However, it remains highly useful to have PMs retain the email reply ability. These function very much like emails already, and forcing users to visit the site to respond increased friction and is quite counter-productive.
I note that the default delay before emailing a notification for a forum post is 10 mins (which increases the risk of missing a recent reply when you post by email), while it is only 20 seconds for a PM. So we already handle these differently anyway. Why not go all the way?
Also, we haven’t got reply by email for chat. Is there a reason for this?