This comment strikes me as far too cerebral. Exercise has demonstrably positive effects on not just mood (the sense of well-being, as you said), but cognitive function, physical performance, and longevity. If you go for a run in nature, you get a boost in creativity (http://journals.plos.org/plosone/article?id=10.1371/journal....). Exercise is often social and can be used to network.
Exercise isn't just a calorie-intensive vacation for your brain, it's an overall enhancement for life.
Excercise also causes stress. If I go two days without running, I feel in a low, agitated mood while at the same time physically lethargic. All throughout the day I have urge to lie down and take a nap. It's exactly like withdrawal from a drug. It starts on the first day off intensifies on the second day. Even a short run helps; for instance a single hard 800 m repeat. After that I feel normal, like on running days.
The problem goes away after a week or two if I quit completely; it's caused by the exercise.
Basically all the strictly positive stuff you hear, though not wrong in and of itself, is a rather unbalanced view spread by people who don't actually exercise, or not a whole lot.
Exercise isn't just a calorie-intensive vacation for your brain, it's an overall enhancement for life.