Ok, i will try to explain how material work:
1) The plugin collects all the materials assigned in the Geometry List (material slot), and creates a multi-sub. It uses instances of the original materials.
2) This multi-sub (automaterial) also includes one standard mat for each color ID of the list. They are used only for display purposes and have not effect in render.
3) The automaterial is assigned automatically to the Forest object, and rebuilt when needed (for example, if you assign a new material in the geom list).
4) The "Reassign" button should be used only if you accidentally assign other material to Forest. In this case, the automaterial exists yet in the scene but it is not assigned to Forest.
So, the right procedure to change a material should be to replace it in the Geometry List. I suggest not to modify directly the automaterial because this would create unexpected results. Anyways it's safe to edit the automaterial in the material editor, and change the properties of the sub-materials (since they are instances of the original mats), but not replace or overwrite them.
Should not be problem with the net paths, since Forest doesn't modify the textures. It only creates the automaterial, but the source materials and their maps are preserved.
About the matte passes, i forward you question to our 3D artist (he is out of the office until Monday). I'm not expert in this field, so i don't want to give you a wrong reply.