Stress can inhibit neurogenesis (among other things) in the hippocampus, as the article states. Is it possible that HIIT was not as beneficial for the rodents, because they were, unlike the moderate exercisers, forced to exercise? Being forced to exercise intensely might have been the real source of stress.
This struck me as the most important potential difference -- that the moderate-intensity rats were able to make choices about when and how to exercise, while the HIIT rats had exercise forced upon them.
It reminds me of Rat Park -- when you stress out rats by treating them poorly, all you end up measuring is the effect of misery on rat physiology.