It doesn't seem as if the article is proposing that training for a marathon will considerably improve your brain functions. I, of course, can't say this for certain, because I'm only able to read the Abstract right now.
What it does
say, however, is this:
That clearly states that the act of partaking in long endurance running affected (notice the past tense used here, and in the article when stating "evolved"), and increased, the general functions of our brains during our evolution. As I'm sure you know, evolution doesn't happen to one single individual over the course of their lifetime. This is merely stating that there is evidence suggesting that long endurance running affected how our brains evolved. It's not saying that running will immediately alter our cognitive abilities.
To me, the article seems interesting because our increase in brain size appears to merely be a byproduct of an increase in stamina, and that humans with better stamina had more access to food, and thus, following natural selection, humans with better stamina passed on their genes rather than people with worse stamina, who also, as a consequence of their lack of endurance, had a less noticeable growth in their brain functions.
This is made apparent by the statement, "This hypothesis suggests that a significant portion of human neurobiology evolved due to selection acting on features unrelated to cognitive performance."
Maybe our larger brains weren't viewed as highly in evolution as we once thought, and our physical abilities took precedence? Interesting stuff.
EDIT: I suppose a more direct answer to your original question would be that the brain simply grew. From what the Abstract states, no individual cognitive performance benefited solely, but all processes increased as a whole.