Mutating a SHA-2 input would allow us to have multiple hashes for a single input, would this increase SHA-2's security?
Arbitrary mutation protocol is equivalent to a random permutation (i.e., a random invertible function); so running through $M$ is basically equivalent to encrypting with some random key $K$. You don't need something so complex as a permutation - you could be adding on a fixed prefix, suffix, etc, just as well.

From a hashing perspective, there's no real reason to do this.
Your chances are already $2^{-256}$ anyway for a collision between two inputs (more inputs increase the chance via birthday).  For each change you do and output you're basically increasing the bit-length, so $2^{-512}$, $2^{-768}$, etc. (so you are increasing security). But you could just as well just use SHA-512 if 256 bits isn't enough for you (and it generally runs faster on modern processors)