Nice article. One of the things I used to do in the past was adjust my CCD settings based on the velocity of certain objects. Some objects would be tagged with different levels of CCD, so high‑speed bullets in the game would automatically get a more frequent raycast-like series of collision checks. Obviously, this comes with a pretty big performance hit if you apply it to everything.
But in games with more open physics sandboxes, obviously more difficult to predict which objects might end up needing it so I used velocity/acceleration as an approx metric to dynamically crank up CCD levels for them on the fly.