To answer the original question, the strange cities of license for some stations are a combination of history and the FCC living in a fantasy world.
History - As some have stated, stations usually had smaller coverage years ago, before they upgraded. It should also be noted that the rules were devised mostly from 1917 to 1934, when the concept of suburbs was virtually unknown. Most people lived in the cities where they worked (except for a few very close-in places just outside of some city limits but on the streetcar routes), where their families lived, and where they had always lived. There were no expressways, even for those who did have cars. Local telephone calling areas were smaller, and long-distance was expensive. If you lived in Miami and had a cousin in Ft. Lauderdale, he was an out-of-town relative whom you wrote to instead of calling, and saw on special occasions. Today you would have each other on cellular speed-dial with unlimited calling and get together anytime.
Back then, it was not too far-fetched to imagine that each town needed its own "voice", and that a Ft. Lauderdale station differed from a Pompano Beach station, from a Miami Station.
Fantasy - Regulators seem to think the world still works that way. I suspect that the public appetite for Coral Gables specific programming is rather limited even in Coral Gables, since people mostly consider themselves part of the Miami region, rather than strictly "locals" in one town. In the eyes of the FCC, WMXJ (102.7) exists for the purpose of serving Pompano Beach -- in the real world we know that the station, like the community itself is simply a part of South Florida. Despite the obvious silliness of this approach, there have been few signs of recognition that people live in Metro areas today, rather than towns.