I think this is highly interesting, but while reading the comments here, I think one should be very careful about the actual content of the paper. It is deriving results about the (phenomenological) master equation. It has been some time since I have studied this, but we are not talking about some first principles theory here. It is possible to derive master equations in some limit from a fundamental theory, but the setting here is purely phenomenological. I.e. the hidden states would be anyway present in the fundamental theory and would be lost due to some integration and limit process in order to arrive at the master equation.