I'm glad to see someone taking that info constructively and wrapping their mind around it.
A couple of things as this applies to the inline 6.
The Datsun L-6 headers, (6-into-1, or 6-into-2, or 6-into-2-into-1 design), already has its exhaust pulses merging at even intervals, giving the L6 exhaust note its smooth crisp tone. For a 6 into 3 header design, (whether it is 6-into-3 with triple exhaust pipes or 6-into-3-into-1 single exhaust pipe), your pairing of cylinders is correct in pairing the opposite firing cylinders, 1-6, 2-5 and 3-4. But I don't think it will change the tone of the exhaust note any from the standard 6 into 1, or 6 into 2, or 6 into 2 into 1 designs. I short, so it wont make it any smoother or crisper sounding. Though having 3 exhaust pipes would be rather unique and exotic looking. If for nothing else other than begin different, triple exhaust could be tastefully ran out the back. Would definitely get a bit of attention at the car shows.
Though if you merged cylinders that fire in odd patterns, (such as pairing 1-2 or 1-3 or 1-5) you would get an odd rough tone like a V-8, Suby 4 cylinder or maybe the Audi 5 cylinder/Dodge V-10, depending on when you merged, which cylinders. (I personally don't like the sound of free flowing exhaust systems on Audi 5 cylinder or Dodge V10! Sound too much like a really old odd ball tractor, not a sports car or even a muscle car!). From an exhaust scavenging perspective, it wouldn't be ideal, but just as the Subies and domestic V-8's with their odd paired exhaust pulses, the merging of odd firing pulses isn't going to "hurt" performance to level you would notice.