Clearly, I’m late to the game on this thread.
For those that use Devon think, I rekindled the DevonThink annotations export discussion a few weeks ago: Revisiting Devonthink Annotations to Tinderbox - #12 by mdavidson.
@Pete came to the rescue and build an Apple Script for the community. See the post. You can now pull highlighted annotations out of your DevonThink PDFs and get them into Tinderbox. It works great.