I really dig this.
Regarding
What is a good baking workflow in a scene with potentially many objects with many texture layers? In a dedicated texturing application there is a clear export step, but how can we make a good workflow in Blender where users must know to bake textures before moving on to the next object?
If Blender is meant to have some sort of interop node system to replace the static export concept at some point (notably for USD), I would say baking fits into this idea pretty well. Define jobs, bake and export all at the click of a button or at intervals…
In any case, I like the idea of encapsulating node trees into layers, bit like geonode trees in the modifier list.