No, but you can still accomplish what you want. Annotations become part of the PDF file on disk. But they're stored as separate editable objects in the PDF tha

No, but you can still accomplish what you want. Annotations become part of the PDF file on disk. But they're stored as separate editable objects in the PDF that remain editable; for example, if you open an annotated PDF in Preview (on macOS) or in Adobe Reader, they are still editable. And so you can remove them. Devonthink also lets you remove all the annotations. With your PDF(s), select Data > Convert > "to PDF without Annotations", and it will make a copy that has all the annotations removed. I agree that it would be nice to keep the annotations separate. But fortunately the PDF format is flexible enough that it can preserve the annotations and not "hard code" them into the visual tree.