To BSC:
Just as we use wood to build our home the Shapers use living tools to work. Just as we have guard dogs the Shapers have pylons. I have not see a reference to the more simplistic creations having consciousness. I do remember reading somewhere that the spore boxes have feeling, or at least they are aware of being touched.
My guess about the plants being capable of different defenses, and the mines being different levels of explosives is just that. Maybe they are different breeds.
In GF1 the Shapers said they did not know about the Scholai. That implies that the Shapers have not explored the entire world. It seems they go place to place destroying than barring locations. Maybe they discover new lands when they close old ones.
I don't remember hearing about birds. I certainly haven't seen any if they do exist. The only livestock seems to be Ornks. I guess they live on pork, green, fruit, and bread.
Shades are simply spirits. What rights do the dead hold? If they attack you they are angry spirits, but I never attacked a shade that left me alone. The shades in GF2 in the pit of the bound one were prisoners. They were contained spirits that wanted to be free. It seems to not exist would be preferable to being an eternal slave.