Mmm, I'm not sure I see what's confusing about it. Once familiar with the format (city, county, state, country), if there are only three elements (in this case Cook, Illinois, United States) that the first is a county; and if only two elements (Illinois, United States) that the first is a state.
If one followed the logic you propose, shouldn't we then expect to see Chicago city, Cook county, Illinois state, United States country? (I can't help but think that's the logic the standard creators used...)
And whatever we individually think about it, it is a standard with increasing adoption "out there". (Some sites reverse the order: Country, State, County, City...)
That doesn't mean wikitree needs to change how it names categories-- especially as Philip points out, cities are categorized within a county category (which I didn't know before). This standard is more relevant for contents of the Place fields.