I still haven't found a way to represent the proposed BEER folder structure using blender's interface.
Here are some of the mockups I came up with, anyway.
1) Everything is bundled in a single panel, allowing for other panels such as transparency, mirror, shadow.
2) The shader layers are arranged in a definite order and cannot be re-ordered by blender or by the user (unlike individual blender panels).
1) The modifiers have to be contained within the box of the shader layer that they influence in order to avoid confusion. The problem here is that there are certain restrictions as you go deeper and deeper into the hierarchy of blender ui elements (eg. column > box > column > box will not work in blender. Notice how the modifiers have no distinct header region)
1) Shallower hierarchy of UI elements allows greater flexibility. Notice the modifiers have a distinct header region since they are not contained within a parent box.
1) Shader layers are organized in panels. The user can easily re-order the panels without BEER ever realizing the difference. Remember, BEER is supposed to use a bottom-up order. This can easily become a huge source of confusion for users.
2) BEER has no control over the ordering of its panels. Since blender uses a first-come-first-serve approach, any new shader layers will be added straight to the bottom. this is the opposite of how BEER should work.
3) This approach will require generating and registering python classes in runtime.
Personally, I like the look of mockup B but i think A is more practical.
Also, I really don't see need to bundle shader layers into folders. There doesn't seem to be a practical way to do this in blender.