Is it possible to improve Paperpile with this kind of tool: Tag, Search & Summarize.
So, in a single document you have multiple points spanning a wide range of topics. Tag, Search & Summarize allows you to tag specific parts of your notes, to later access them for a given topic, across and within all documents. May be that could be possible by tagging the highlights or the notes.
I have requested something similar. Paperpile will be THE perfect reference manager if they add the functionality of tagging, organizing content. Currently, I use Power Notes extension and then export into excel to organize my Lit Review.