What do you mean by global state? If you mean the implied global object (window in browser or global in node) then they are not the same as a global state in Flux/Redux architectures.
Either way, the general rule of not modifying something globally available is to save from unintended consequences like naming conflicts, overloading, or mutating shared objects between implicit dependencies. In Flux/Redux the state is meant to be shared across the app and so therefore there are no unintended mutations since it's understood that's what the state is there for. Think of the state as a sort of light, client database for your app.