"Works of art make rules. Rules do not make works of art."
-- Claude Debussy
The rule book is and always has been a friend ... a system of common practice derived from the successful workings of a vast number of Western composers on back through many centuries of music writing.
The rule book then, as thus defined, is in place to guide and serve composers of the present day, not to intimidate them, not to enslave them, not to be poised ready to crush them in an instant for the slightest deviations.
In the case of organ composition, composers first learn the rules and learn to live within the limits they impose so that, if the opportunity ever happens to present itself, they will know how to bend or break one of those rules like an artist.
It's a provable fact that no composer of eminence ever arrived at a level of ultimate mastery without having passed through a period of strict discipline with respect to the rules of composition and part writing ... just the sort of thing one would find laid out in the rule book.
It's also a provable fact that the artistic bending or breaking of a rule, at times, can lead a composer to discover beauty where they were told, or led to believe, that there was none [See blog, Monotony, Getting Started With Writing, Part XX].