I would greatly hope that three apps should work together seamlessly to recognize each others annotations to PDFs on the iPad: Highlights, Devonthink ToGo, and Bookends. Why? Their approach to annotations are nearly identical (I think that BE and DTTG simply used exactly the same underlying tools). But they do not work well to share. The annotations do not get transported properly among them through the share sheet. Sometimes they are. But most times they are not.
Who is the bad guy? Not sure. Perhaps this has to do with the different storage locations for each, either in iCloud or in local (or in both).
I have tried one to one and one to many options. In BE, my PDF will sometimes simply disappear and will be impossible to recover back. In Highlights, I end up with multiple time stamped versions of the same PDF document in the Recents list. I can documents into DTTG but I cannot seem to get them to go back out right.
I raise this observation perhaps as a challenge. Maybe something fundamental about Apple Share sheets is not going to make my dream happen. Or maybe something is wrong with how Highlights and Bookends handle the PDF share while DTTG has it down perfect (I have sent notices to both apps as well).
Each of the three apps have their strengths that are best handled by each separately. I really would like to see this ecosystem work well.