Respectfully, I disagree. I understand people have vastly different experiences and preferences. In my ideal world, a PR is a unit of work that has an in-state and an out-state. I don't have to see an initial commit within a PR with a full fledged spec and then wonder if any future commits within the same PR overrode those changes. A PR will rarely be clean from the start.

The way it appears to me, if there's multiple commits submitted as separate PRs, then maybe the PR wasn't so atomic to begin with.

Indeed, I agree. If a PR has multiple commits and those commits are atomic then by definition the PR is not atomic.