A lot of times it is simply following some geographic boundary that is obvious locally but not on a map like this: a river or whatever. Even if the boundary isn't itself a major obstacle now the settlement history is embedded in the social geography.

Or like look at that corner of northern indiana. That's the part of indiana that is part of the chicago metro area. Makes absolute sense to avoid cross-timezone commutes.

Northern michigan is pretty damn far north! Winter sunsets up there would be before 4pm on central time. Makes sense for them to shift it permanently.

I think they probably all make sense if you know how to look at them right.

Yeah, good point - I assume a lot of the seeming anomalies are due to conurbations that, as you say, aren't obvious when just looking at borders.