Even though the list does include some foreign and historical usages, most are references to current day English usages. I find it rather silly myself that's why I prefer to use biology rather than gender when referencing people; evidently there are countless genders but only 2 biological distinctions. Ya can't mis-gender someone if you don't reference their gender.
I don't know how much biology you've studied, but I think you've got it backwards. The biology can be much more complicated than you think, and people actually depend more on phenotypic than genotypic characteristics to define social groups. That is, superficial characteristics are more important in categorization than underlying biology, which itself can be ambiguous.
Linguistically, it also gets complicated, because there is a difference between grammatical and semantic gender. English tends to rely largely on semantic gender, but many languages make grammatical distinctions between male, female, and neuter nouns. (For example, "the moon" in French is feminine
la lune but masculine
der Mond in German.) Worse yet, masculine and feminine nouns can be at odds with semantic gender. So the word for "man" in Polish is feminine m
ężczyzna, but you have to use masculine adjectives and pronouns to modify or refer to it.
Gender reference in English is much simpler semantically, since we don't have gender classes for nouns, but pronominal reference is a grammatical feature of the language. Hence, plural third person pronouns like
they can be occasionally be used for semantic singular reference under certain circumstances.
In summary, pronoun reference is quirky in most languages, and it is far from being objectively biological, as you and
@Shaul have been claiming. Speakers of a language develop conventions of usage, and those can change over time, especially when cultural and social conditions change.