If I were to explain it logically, I would have to say that as Fluttershy slowly moves through the mountainside her skin gets pulled outwards from her body. It is a basic biological fact that skin can grow/expand if tugged over a long period of time. That means when Fluttershy is in the mountain her skin, organs, and bones are spread out into the shape of a tree. However, the instance she leaves the mold, she would collapse into a fleshy blob and probably be in a lot of pain.



That's the price of following your dreams.