In quantum mechanics it is usually the case that when degrees of freedom in a system are traced out (i.e. ignored), the evolution of the remaining system is no longer unitary and this is formally described as the entropy of the reduced density matrix ($S = Tr(\rho\ln{\rho}$)) attaining a nonzero value.
Why is it then that there exist certain quantum mechanical systems which have unitary evolution, but for which we clearly do not keep track of all degrees of freedom? Practically any non-relativistic quantum system such as atomic structure, spin chains, any implementation of a quantum computer etc. are clearly just effective theories which ignore the massive number of degrees of freedom underlying the more fundamental physics, i.e. quantum field theory. But somehow we are able to trace away all of this underlying physics into an effective potential/interaction term in a Hamiltonian and thus retain unitarity.
Now this does not work entirely for all systems, particularly it is impossible to hide away the full coupling of an atom to the EM field because you have spontaneous emission, a non-unitary effect. But still a large part of the electron/proton interaction (which is really mediated through the EM field) can be captured by the Coulomb potential, which ignores the EM field yet is still unitary. On the other hand, some systems, such as certain implementations of quantum computing/simulation claim to be able to achieve perfect unitarity and are only limited by imperfections in the system. At least, I have never heard of anyone talking about intrinsic unitarity limitations to a quantum computer.
My questions are:
-Under what conditions can underlying degrees of freedom be hidden away into a unitary interaction?
-Are there intrinsic limits to unitarity of any quantum system (such as an atom's unitarity being limited by spon. emission), assuming that you will always trace out a portion of the underlying field theory?