In counterpoint, the functional independence of voices is the prime concern. The violation of this principle leads to special effects, which are avoided in counterpoint. In organ registers, certain interval combinations and chords are activated by a single key so that playing a melody results in parallel voice leading.
While counterpoint emphasizes the independent functioning of each voice, violating this principle leads to unwanted effects.  In contrast, organ registers utilize specific chord and interval combinations activated by a single key to create parallel voice leading when playing melodies.