In abstract (deterministic finite) automata theory the set of states of an automaton is an arbitrary set Q, and the transistion function is a specific set δ ⊆ Q × Σ × Q (with alphabet Σ, i.e. another set).
In a "real" automaton - seen as a dynamical system - its states are configurations of the system. These configurations may determine the transition function - seen as a dynamical process - in a traceable way.
I am looking for references where the states of an deterministic automaton are treated or at least discussed as configurations of a dynamical system - and not only as arbitrary atomic entities (symbols). Where should I look at, how could I search?
You might be interested in the following papers. I suggest you to read [2] first: it is shorter and more elementary than [1].
[1] Béal, Marie-Pierre; Perrin, Dominique. Symbolic dynamics and finite automata. Handbook of formal languages, Vol. 2, 463--505, Springer, Berlin, 1997.
[2] Perrin, Dominique. Symbolic dynamics and finite automata. Mathematical foundations of computer science 1995 (Prague), 94--104, Lecture Notes in Comput. Sci., 969, Springer, Berlin, 1995.