Ok, I was confused because if you say “Consider a system that transitions from energy state 0 to an adjacent energy state 1” it sounds as if the energy of the “system” is changing and when you say that “a particle [...] can be in two different energy states at the same time” it seems that you are referring to the atom being in a superposition of states with different energy.

One can speak meaningfully of "an atom in a superposition of energy states" despite the fact that, strictly speaking, such a thing is not possible, just as one can speak meaningfully of "the force of gravity" despite the fact that, strictly speaking, there is no such force. The latter is understood as the force-like effect of curved spacetime, and the former is understood as "an atom being a component of a system in a superposition of states with different distributions of energy" (or something like that). Communications between humans becomes more productive when we cut each other a little terminological slack.