Hey! Why not all let's gang up on Vaughn?
Seriously, all he is guilty of is questioning "facts" that do not (to him) make sense. I think we all have that prerogative. What complicated matters is his bullish stance on his beliefs. Strangely, no-one has given him all the facts (or, rather, they have not been pulled together into a coherent picture), except point out to him that he lacks complete understanding of the subject. So, here, let me try...
1. (Martin pointed out that) ports produce non-linear distortion.
2. The thing about non-linear distortion is that it produces harmonics. These distortion products are not band-limited, as they have their own generation mechanism.
3. These distortion products are not resonance-based (else it would linear distortion), but related to the acoustic interfaces that the port sees. If they were mere resonances, then Vaughn's assertion that band-limiting would solve the problem would suffice (but see point 2.).
4. To filter out the harmonics (2.), Hennie pointed to acoustic filtering, and also to its non-feasibility (at the frequencies involved).
Does that sum it up?
Next question: To what extent does port flaring ameliorate the problem?