I’ve read through the suggestions. The “low-floor” use case is just drawing a health bar that would not ever be covered up by any sprites. Other people just wanted to be able to draw on top of sprites. And other people wanted to change something in their drawing without having the overhead of redrawing the entire stage in an pen-based animation.
I think what you are suggesting would cover these and provide a useful upgraded feature.
Please consider adding an option in your Pen Extension to allow a sprite to draw at its own layer instead of always drawing on the stage. This is a frequently asked for feature in the Scratch forums. It would enhance the ability to use sprites with pen drawings.
To go along with this suggestion is also a request to provide a “clear pen drawings for this sprite only” feature.
Both of these would give creators the ability to make and modify their own sprites in real-time using their programs.