Having the same message content arriving with two Message-IDs is a bit worse than just the user seeing both copies. It causes email in-reply-to chains to be broken if the user happens to reply to the wrong one. They'll end up replying with a message-id that nobody else has seen. Many email clients will consider this a new conversation thread, and separate the messages from the rest. If this happens enough, it can really fragment a conversation.
David
David Brown