The issue, at least for me, isn't that it makes it impossible to figure out how many characters a ligature is (since, as you noted, it doesn't), but that it adds some ambiguity, especially when taking a quick glance. Ambiguity can slow down parsing (in the brain) and potentially lead to errors (in the code) if I mistakenly think a ligature is a single character.
For instance, in the examples from the article, the == and -> ligatures in particular look like something I might not always see as two characters.