All of the advantages, like "it’s a simple threaded discussion between stakeholders, centered around a topic", is exactly why people like stacked diffs over PRs.
GitHub is doing "stacked PRs", which is like stacked diffs but more like PRs in the sense that they're stacked branches rather than stacked diffs. I agree that this seems less ideal, but they also are putting it into an existing project, rather than rebuilding everything around it. There's pros and cons to both approaches, but I agree that I'd prefer a native system built for this, personally. I'm still glad they're going to be popularizing the general concept.