I'm not trying to be dense, but I still don't see it. Punctuation helps with identifying boundaries of clauses, whether they're dependent or not, whether a sentence is a question. Is this what NLP struggles with? I don't think so. One of the big unsolved problems is understanding the referents of pronouns (and other proforms, like "I will [do so] too"). Style guides and generally prescriptivism does not help that.

Another ambiguity is parse ambiguities like " I saw the girl with the telescope." What does "formal" English say about that?