PDF is designed for annotations in the file format. You annotate in one editor, you can change the annotations in another. You can always distinguish between original content and annotations. I see no indication that Okular stores highlights or annotations in a separate file, that would be bizarre.
There is no mechanism for annotations in HTML or the other formats I listed. An editor would just be editing the original content in its own non-standardized, non-portable way, which is not desirable for a number of reasons.
So when you say:
> What you are describing are features of an editor, not a file format.
That is incorrect. It is an intentionally designed and standardized feature of the file format.