In the example: "small refactor 25LOC -> new API 500LOC -> migrate API users 50LOC"
Making a PR of the small refactor will probably garner comments about "why is this necessary".
Opening two PRs at the same time is clutter as GitHub presents them as separate.
As well, sometimes CI won't pass on one of the stages meaning it can't be a separate PR, but it would still be useful in the code review to see it as a separate stage.