Thanks for the tip on KOReader. That looks promising (although features list says it doesn't support notes, yet) as the kind of open-source app I was thinking about. If they can add notes support, theoretically you could run this on Kobo and Android devices and sync your reading data to some external shared location like Onedrive, Dropbox, or Gdrive.

ETA: Would also be cool if it implemented PC/Mac or better yet, web access mode for universal access. I just installed KOReader as well, it is cool but it is struggling with extremely slow performance on some larger epub files.