"An atom can be described by its quantum state only if it's isolated and in that case its energy is constant."
How do you figure? As a contradiction, take your atom+electromagnetic field system, describe the transition from excited atom to unexcited atom + photon state, and project out the E&M field. Voila, now you have a quantum description of an atom transitioning between different energy states. Its dynamics may look funny, i.e. they may appear nonlocal, they may not conserve energy, etc. but that's different from saying "there is not a quantum description of these dynamics" which is what you're claiming.
How do you figure? As a contradiction, take your atom+electromagnetic field system, describe the transition from excited atom to unexcited atom + photon state, and project out the E&M field. Voila, now you have a quantum description of an atom transitioning between different energy states. Its dynamics may look funny, i.e. they may appear nonlocal, they may not conserve energy, etc. but that's different from saying "there is not a quantum description of these dynamics" which is what you're claiming.