As you have described this, it sounds almost related to bookmarks or a special way to comment. Essentially a bookmarked region and potentially a automated heuristic to automatically make certain types of these regions.
Also related is 3.1.b of this My First Impressions post.
The regions could either come from some sort of markup in comments similar to markdown or color region info could be stored in a separate file though that might make things tricky if you wanted to share them with others or check them into version control.
What we want to evolve the SkookumIDE to is something like frame-based editing. Though not exactly as the Greenfoot team at Kent University describes it.
Basically the idea is to keep the language just text though to have the SkookumIDE color blocks of code and maybe allow more building block mechanisms such as Scratch or Blueprints.The extra graphics and visualizations would just be visual layers over the text as a hint or aid.
Example of some Scratch blocks.
It would be different in Sk particularly since it would always be layered on top of human readable text. Most of these systems are binary or have text that is not really meant to be edited by humans.