Can I open/annotate my documents in a third-party PDF reader?
Not at the moment. Paperpile comes with its own reader/annotator (can be switched on web via Settings > Browser Integration) and supports Google Drive and Chrome's default viewers.
It is possible to sync via Google Drive as this cloud storage system was designed exactly for the purpose of sharing access to files between web, mobile and desktop.
We know some users manage to configure their preferred viewer as browser default and open Paperpile files there, but annotations made over there are not visible in our servers. Similar limitations exist on mobile, where application sandboxing can complicate file sharing across apps/programs further.