OK, I am not Onyx, but I think that if split screen for scrible (or better pdf) is possible then the functionality you ask for could be implemented in following way.
During the work there would be possibility to add/modify/delete "side notes, clippings and scribles" in embedded window. And the reference from which page you "jumped" there (to which part of text it refers to) would be recorded. And similarly like with normal scribles now, it would be possible on user's demand to create a new pdf with scribles, notes and in appendix also those "side notes" referenced by shortcut from place of creation and referencing to place of creation (It would be possible to jump from text to appendix note and also from appendix note to page it refers to).
I guess it could be done. I have no idea how much work it is and if embedded editing is possible with reasonable amount of effort.