Will some things filter through this list? Undoubtedly, but I would be surprised if it's a significant percentage. Extremely high-volume lists probably need some more specific care, to be sure.
Couldn't you filter most of them out by the timestamp? If you get a reply that was sent faster than a human could have responded, ignore it.
The auto-reply is probably sent by a desktop email client, which are often offline and/or configured to only check for new email every few minutes. So you'd fail to mark a lot of auto-replies.
Exchange configures it on the server because generally people have their computers turned off when on holidays.