Ah, but the mental midget was not dealing with issues in his access to root, but the ability for the human brain to truly separate it's self from it's data input.
Just as the physical body will die in the real world if the virtual body dies in the matrix because the brain is not able to distinguish between the two and thus believes it is in fact dead.

Being able to dodge bullets and fly are just examples of things that Neo was able to "recode" his brain to believe.