Is there some example of embedded discourse? As a general discussion forum it's quite bad, but seems ideal for this kind of stuff (as an alternative to disqus). Additionally, are there providers of discourse, either paid or ad-powered, so people don't have to take care of it?
I've read some reasoning about that when they introduced the product... and it wasn't convincing (something about keeping discussion on topic I believe?). I really think their reason is ease of design, implementation, maintenance and scalability.
I dunno, I think they actually believe it, and they do have some experience from the SO days.
Threading has its place, but creates sub-discussions, something that is understandable to want to avoid if your vision is for more inclusive conversation.
That said, in higher traffic forums I see this approach being a nightmare to keep up with, and will read like a schizophrenic journal.