Except that in usage it's almost never unclear and the use of 'literally' in place of 'figuratively' adds emphasis. So if anything it adds meaning. "Literally born on the track" is a good example - the meaning is clearly 'figuratively'. And the image of popping out of the womb onto a running surface adds emphasis and humour.

Contronyms - words that can also mean their opposite - are just a phenomenon of language. Cleave is the common example. You can cleave to or cleave in two.