It is a neat trick, and not something that happens often, but I would guess that’s because it’s not useful as anything other than a neat trick. I’m not seeing the eternal golden braid in it, is all.
Actually, if Bach had kept the pattern intact without “crossing the enharmonic seam” it wouldn’t be much of a loop at all; the piece would end up in B# minor after six repetitions.
(edit: sp.)
Forgive my ignorance, not having read GEB, but I can’t help being underwhelmed by the Bach example. This Youtube video plays the Bach canon in question. The canon begins in C minor and modulates up in whole tones until it arrives at C minor again an octave higher (the Youtube recording returns to the same octave, but it does so using trickery—notice that in Bb minor, the sixth time through, it ends on a D notated a ninth above the next C but sounding only a step above it).
Unless I’m missing something, this is rather like saying that if you walk for ten hundred-metre lengths, you’ll end up a kilometre from where you started. Yes, you will, but so what?