Interesting. I would add that in all size groups, perfectly reasonable people with good ideas, even the best ones sometimes, get marginalized. No doubt you've thought of this, but it seemed to be a blind spot of the article.
Another, the 'master manipulators' bit. I think only at the margins. I just think many of the lessons of deception are lost on modern man, and so there is free reign for a larger percentage of the triads than there would typically be in a working society. For the most part, there are a lot of wannabe manipulators who use low skill techniques. It's not lost on me that, the larger the group, the easier it is for them to find low skill victims. But I think the real dark triads are also easily identified under a bright light too, and too often given more power than they are due - villainy is glorified and ascribed intelligence. The reality is that it takes a broken personality and a broken mindset to be capable of such deception. Broken people leave the signs of... brokenness.
Also, it is the very lessons of game theory that show why dark triad is an achilles heel for them. They don't get to play just one game. They have to uphold reputation. In larger groups they get cover - they can travel with the circus. But technology is catching up to the mean, where it will be much easier to spot.
I think dark triad has an advantage, but a larger disadvantage. It requires a faith in humanity to agree - a belief that good works better than evil, that it is a choice we all make, and that it is nature over nurture. It is only in these weird times where triad has an advantage that bears fruit. But they pile up that fruit, and it rots in time.
I agree entirely that a proper economic system minimizes suffering of victims and maximizes regulation of dark triads. That system is laissez faire maximization of individual liberty + educated / high information populace + technologies that empower the weakest among us to participate on a level field.