@kfitz@hcommon, Apologies for the vacation delay...

Yes, you're right that there is duplication. Ideally the webmention receiver would be able to match the duplicate and connect them automatically so they don't display twice, but no one has written code for doing this (yet) in WordPress. In practice, I don't often do this myself or even see long threads like this in the wild. As a result, I don't mind deleting the duplicates manually. I'm only aware of a few implementations of de-duplication in other projects, so it's apparently not been a high priority for others either.