Maybe a partial answer to your question, but if you select View -- Debug Windows -- Breakpoints in the Modeler, you'll see all of the microflows with breakpoints.
Please add you idea also on the Idea forum; https://forum.mendix.com/link/ideas
I like the idea for favorite a microflow or mark for todo's etc :)
If you could add folders (or documents like microflows) to favorites that would be great.
With a tab/panel next to the “app explorer” with favorites. So you can easily look them up.