In this case, the "bubble" is the thing...but yeah, it's a little noisy. Perhaps if we fuzzed out the background a bit when the annotation viewer (the bubble) is open it would help?
It's great that the site supports such deep linking.
Doesn't your suggestion harm the UX for the person who has spent the minute or two required to figure out how to operate the site?
Even from my very first visit earlier today, I found great value in being able to read the annotated code and the annotation simultaneously.