Being clever, but not for the sake of being clever, all of Bach's imitation and fancy counterpoint has purpose. The voice crossings, close ranges, and similar lines may have been the qualities that the early Baroque composers hoped to discourage. And this is not the clarity of voices that is generally associated with Bach. Much of the detail seems to have been written more for the performer than the listener. Nevertheless, it is a complex sound that achieves large scale events. And these events are well controlled because of Bach's clever technique.
David Huron has presented research on the perceptual salience of Bach's counterpoint, though he restricts himself to Bach's pedagogical/exploratory works -- The Well-Tempered Clavier, The Art of the Fugue, and The Musical Offering -- and some of his organ works. Watras points out that Bach's writing for choir and orchestra is perceptually messier, though the technique is still controlled. This is probably due to the larger musical forces that Bach is dealing with, as well as the concerns of text painting.
So Ligeti is not necessarily revolutionary in his approach to polyphony, though he is much more deliberate in his blurring of voices. Maybe instead of his Lux Aeterna and Atmospheres, Kubrick could have used Bach's B minor Mass in 2001 ... maybe not.