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I'm fairly opinionated on that point. I think they should be threaded. I've been stewing on my detest of bolt-on DM systems for years.
If our threads aren't good enough, they should be made better - improving both DMs and threads alike. That assumes the deficit isn't fundamental to DMs being ordered as trees though. But, the average DM UI are lists of messages and lists are trees with only a trunk/branch so we can probably just improve how we display trees in certain situations and get the best of both worlds.
Yeah, makes sense to keep them threaded under the hood. I think it's more of a display hack for detecting what kind of message tree you're in (maybe some node count / max path thing).
My main point is that for a long chain of direct replies, some of the UI features of threading, like indented blocks and max depth, may be UX-reducing
I might add: consider making the UI for DMs unthreaded. Under a threaded UI, long chains of replies are hard to read because of the max depth. This makes sense in a free-for-all discussion, but not so much for a 2-person text chain.