Simple: because it's not supposed to.
Indole and skatole are related byproducts of protein putrifaction which occur in the digestive tract, produced by the bacterial breakdown of the amino acid tryptophan. They are mildly toxic substances and are the source what most people describe as 'fecal odor'.
Skatole comes from the greek root skato -- meaning 'dung'.
When someone eats foods that are high in protein (e.g. particularly animal products but could be any high protein food) in combinations that confound our digestive enzymes and/or in quantities too great for our body to handle, much of that protein is gonna rot in their gut (producing indoles and other fun stuff) and pass through them undigested and unassimilated. You can bet your hard earned dollar (or mangoes if you prefer) that whatever comes out the other end is gonna smell like a classic #2.
If you eat foods which are optimal for our digestive physiology (i.e. fruits and veggies), in good combinations, and your digestive tract is functioning relatively well, your body ain't gonna be producing very much if any indols and skatols. Hence minimal odor, if any at all. This is what's healthy, what should be normal.
So there you have it.
Btw indols and skatols aren't the only thing putrifactive bacteria like to cook up in the gut of a SAD eater. Those fragrant substances interact with other chemicals to create even more toxic stuff which is absorbed into the bloodstream. Protein putrifaction also produces carbolic acid (used for lethal injections by nazis amongst others) hydrogen sulphide ('rotten egg' smell) and methane (contributes to global warming lol). So it's pretty much a microbial hoedown in the gourmand's intestinal tract and all the stinkiest toxins are invited.
Physiologists actually know about all this stuff. They tend to think it's all 'normal' since it happens to virtually everyone on the western diet, assume the body 'adapts' to these toxins, and that they may even play some important role in metabolism. Whatever, doctors believe all sorts of silly things, don't they? :)