The short summary is that aerobic exercise performance in humans is limited by the maximal rate of oxygen uptake or VO2max. Oxidation of fatty acids requires more oxygen per unit of "energy" produced than glycolysis; they are simply less bang for buck (or oxygen). Hence chronically depleted (particularly muscle) glycogen stores are a great recipe for bad exercise performances as you force the body into deriving more energy from fats.

Now, in reality, energy during exercise is always derived from a mix of both fatty acids and glycogen. In general, as exercise intensity increases (you are getting closer to VO2max), a larger ratio of energy will be derived from glycogen. So for your friend, running 54k of mountains is only going to be done at rather low intensity (50-60% of VO2max), where ~60% of energy will be from fatty acids, saving glycogen and preventing hypoglycemia.

Hypoglycemia, incidentally, is also known as "bonking". It's rather unpleasant. On long, high intensity exercise sessions you can't usually replace all the glycogen you deplete through food intake. So if you start with lower glycogen stores through a low carb diet, what you are doing is priming your body for hypoglycemia.