It's not the only element of style that may seem illogical, there are many more. Off the top of my head:
* Nested parentheses. (In theory, you could use any level needed (provided that they make sense), but in practice, they're scoffed at.) It is similar with quotes, for the same reasons: limited readability - although here you can at least juggle with single, double and French quotes, depending on the language and style guide used.
* Repetitions: unless used as a stylistic device (in poetry, advertising, etc.), your editors will try to modify repeated words, trying to find synonyms. In technical writing, it is an abomination, and competent editors know very well they must not touch any specific terms, no matter how often repeated, as they have very precise meaning.
But in general, the rules present in style guides are meant to ensure consistency and uniform reading experience, so that the reader is not distracted by form and can concentrate on the meaning, so they are a good thing as long as people are aware these are just arbitrary rules separate from spelling and grammar.