Bump! I would also love it if the general notes from Paperpile continued to be visible in MetaPDF. While I sometimes want to make embedded comments, I also like to have an overall notes section for the article (and some basic formatting features would be especially awesome). I love how the classic PDF viewer has this as a floating window in the corner, with the content also visible in the main Paperpile reference library. I currently copy and paste notes from Apple's Stickies as a workaround.