Heh. Well, I thought that taking annotations front-to-back would be sufficient, but it finally happened: I tripped myself up with the front-to-back heuristic.
This weekend, I read through and annotated an article, failing to realize that I had added a highlight to the article’s conclusion in the past. My beautiful stream annotations workflow therefore produced a few extracted notes—mostly of the same annotation! D’oh.
This morning I played around with some options for interacting with each annotation via AppleScript. Sadly, there aren’t many: I could open the file in other apps, but that makes the automation more complicated and less invisible. It seems like the best solution is to get down to ASObjC and use the metadata there.
Fortunately, I just lucked into a solution for the problem I reported a few weeks ago.
So, my next script-project will be building out a way of streaming annotations in the order they’re added. @cgrunenberg, since I was grateful you warned us of your Sherlocking plans last week, please let me know if summarize-highlights-in-the-order-annotations-are-added is also something you’re plotting to do. 
(That’s not necessarily a feature request… I don’t think it’ll be too hard to do with scripting!)