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Bell's inequality does not preclude all internal machinery of the type that you're describing. It does preclude any mechanism in which the theory governing the behavior of the hypothetical hidden variables is local (where "local" means that the response of a detector can be predicted using only the value of hidden variables in the past light cone of the detection event).Mark Harder said:If, on the other hand the atom's nucleus possessed some internal machinery that determined the atom's fate, then ascertaining the values of parameters that govern the machinery's behavior might tell you when the atom will decay, and it might be a possible to learn how long the machinery has been ticking away. But, thanks to Bell and his theorem, we know that such an internal mechanism in a quantum particle cannot exist because that would entail the existence of forbidden "hidden variables".
Thus, Bell's theorem leaves room for deterministic theories (as well as hidden variable theories that are not deterministic) as long as they are non-local.