Comments on issues use the format <[OrgName]/[RepoName]/issues/[IssueNumber]/[CommentID]@github.com>
A mitigation to this would be to take the combination of message ID and the sending domain and use that as the unique value, because message ID is not guaranteed to actually contain a domain label that's owned by the sender.
For example SendGrid's message IDs are <[RandomValue]@geopod-ismtpd-[Integer]>.