Instead, we got a fake dilemma based on pseudoscientific nonsense by writers that love to throw around the word "evolution" but don't have the science knowledge of a bright high school junior.
Actually the science presented in the episode is consistent with that shown in other episodes.
The episode The Chase put forward that much of the intelligent life in the galaxy was designed to occur. By a early species (sometimes) called the Progenitors.
Phlox might not have known the whole story, but he did seem to understand that intelligent life doesn't just happen (in the Star Trek universe) naturally, but is "preprogrammed' to be the result of the development of certain humanoid lifeforms.
Random selection plays no part.
Phlox's decisions are based upon his knowledge of how things are, observation of other species. Again, Phlox might not have all the pieces, but he does know that evolution of intelligence is something that is predetermined and built into a beings genetic structure. In his examination of the second species (I forget their name) Phlox might
have seen the genetic markers of a future highly intelligent species, more so than with the first species.
You kind of touched on something I wanted to express.. when people diss this episode one of the reasons some give is that they got evolution wrong, and evolutionists (or fifth grade science students) would cry foul.. however.. it's Trek, and while Trek pays service to science, it's fast and loose about it. So that particular argument with regards to "getting evolution wrong" is pretty weak, especially when it could be said that the evolution thing is at least consistent with other Trek canon, as you surmised.
science is never the point: the dilemma presented and how they react to it is