The point of having the relationship between original posts and replies explicitly asserted with Atom Threading Extension is so that feed readers can thread the replies beneath a post correctly, even if the post has already been read. It can be useful when the topic has slipped the user's mind and a reply comes ticking in; he might want to look at the original post again, which he can if the feed reader knows which post the reply he's looking at is a reply to. Without ATE, that's not possible.
With threaded discussions, ATE is even more useful, but it has its benefits in flat discussions as those performed n PunBB as well. FYI, that RFC is as stable as it can get. It has its own RFC number (4685), which makes it "final" in the IETF. I don't have any statistics on how widely supported it is, but the more feeds that incorporate it, the more likely it is that we'll see feed readers implementing it as well. Being able to thread posts and replies is a much wanted feature in feed readers, so I assume that we'll see implementations popping up in the near future.