"Autoantonyms" are kind of a joke, a pun, a play on words. They exist by accident. They're not a normal part of the grammar of the language. Since native speakers are used to the language as it is, it can be a form of humor to point out surprising inconsistencies which we all know, but never notice.
The comedian Gallagher liked to ask questions like "Why do we talk about a pair of pants, but only one bra?"
You might as well ask "why are there so many different meaning for the same word?" For example, "beam" can mean a ray of light, a piece of heavy lumber supporting a house, or the width of a boat.
You might as well ask "why do words that sound identical have different spelling?" "Rough" and "ruff," "pane" and "pain," "meat" and "meet..."
History. Tradition. Accident. It's just the way it is.