Weight loss programs have to focus on preempting and managing appetite. There's a wealth of studies connecting exercise to increased appetite (c.f. OP), especially focused, running-at-the-gym, doing-penance-for-those-donuts exercise. (Low-level activity—walking around, say—doesn't seem to provoke the same uptick in hunger. But it also burns way, way less calories.)
Your counterfactual assumes that the runner isn't more likely to eat an additional 2,000 calories, which is to say, they're already managing their appetite. If you can manage your appetite, then go for a goddamn run already. You'll be happier for it. If you're not managing your appetite, work on that—exercise will not help you lose weight until you do.
There's a great book—The End Of Overeating—which details the intersection of modern food science, evolutionary psychology, cognitive psychology, and human physiology. If you're interested, give it a go.
(BTW, bringing up elite athletes doesn't help the discussion—elite athletes regularly have 1.5-2 times the VO² max of even extremely fit people. Hell, five-time Tour de France winner Miguel Indurain could circulate 7L of oxygenated blood per minute compared with the 5-6L of his competitors and 3-4L for the fitter of us regular people. Human physiology has a statistical distribution, and bringing up people many standard deviations from the mean doesn't help any of us regular schmucks. My mutant power certainly does not involve my metabolism.)