Unlike many United States cities, where a river is no longer the focal

Good question! When we use "like" or "unlike" we have to compare nouns or noun phrases.

For example, "Philadelphia, like Boston, is a wonderful city, but it has an inferiority complex." (In case any Philly people are tempted to throw batteries at me: I LOVE Philly, and have family there. But it totally has an inferiority complex.) In this case, we're demonstrating a similarity between two cities, "Philadelphia" and "Boston." That's fine. What I can't do is write, "Philadelphia, like in Boston..." because now I'm demonstrating a similarity between a city and a prepositional phrase, and that would make no sense.

(B) has a similar problem. Here we have "Unlike the river..., in San Antonio," so we're comparing "the river" and the prepositional phrase, "in San Antonio." Even if the sentence said, "Unlike the river, San Antonio...," the construction still would be wrong, since we'd be comparing a river to a city.

Because (E) doesn't contain the word "unlike", we're under no obligation to compare nouns directly. Instead, we're comparing contrasting clauses, as indicated by "but." Because there's a logical contrast in the ideas expressed in each clause -- in most cities rivers aren't a focal point of life, but in San Antonio they are -- this construction is logical.

I hope that helps!