Regardless of how Discourse handles this, a Message-ID should be unique. In my opinion, when a listserver sends a message to a mailing list, it creates a new instantiation of that message and thus it should rewrite the message ID.
Also, I fail to understand how the original message could be suitable for both members of lists A and B, but the reply of the member of list B could not be revealed to members of list A. If those audiences are that different, why does the user send the same messages to both lists at the same time?
Maybe there is a good technical solution for this and maybe Discourse can be changed so that it handles this correctly, but I find this a really weird edge case in 36 year old technology.