I think you've made an invalid move in going from a theory an earth bound expert could understand to an atomic theory. I don't think being able to "translate" the whatever working theory the aliens use into an atomic theory is sufficient.
So for a perhaps hideously opaque example. Suppose instead of aliens we're talking about teenagers (a reasonable first approximation), teenagers in a high school physics class. I could look at their work with forces and vectors and show how it is equivalent to solving the same problem with Lagrangians and Hamilton's principle. But to go from that observation to making the claim that the teenagers are aware of the concept of action and any of that is a pretty extreme leap, and it would be improper to say the teenagers had a formalized theory of least action.
Unless, of course, I am just wildly misinterpreting what you were saying, I which case carry on, don't mind me.
aliencam: Henry Petroski talks about similar things in his various books on engineering, often technology precedes the science that explains it. For example early aircraft development preceded any strong theory of aerodynamics.
I guess depending on the biological constraints the aliens might not need all that sophisticated of a spacecraft and so that's plausible. Like alien tardigrades or something (the favorite animal of Cosmos).