+1 for a solution that makes it easier to use other apps to interact with the PDFs in Paperpile. I agree with the linked post, the issue with trying to implement all of these features is that no matter how much Paperpile works on things like handwriting with a stylus, dedicated writing apps like Goodnotes are probably always going to do it better (this is not a criticism, these apps are putting all of their resources into giving the best writing experience possible, while this is only a small subset of the many [great] features that Paperpile offers.)
It would be great if you were able to use Apple’s Open in Place API in your application. This allows documents from one app to be opened in and edited by another application, without making copies (according to the linked post, it seems like this is possible in Android as well). Other reference applications like Bookends use this to make it possible to use the share sheet to open up a PDF stored in the reference manager in an application like Goodnotes, write on it, and then save those changes back to the original - without having to worry about dealing with duplicate files. (Edited to include information from the linked post; sorry, should have read it first).