I'm not sure how you get from (1) his logic seems flawed, to (2) he's being disingenuous. Can you please elaborate?
2) He has an preconceived theory of how "ability" and "preference" work. The science does not point to his conclusions, because the science cannot point to any conclusions: ability is simply not scientifically understood or defined at all in the software engineering field, and preferences are barely understood and have many weird consequences (Dan Ariely's work is a great example of this). He is being disingenuous because he is making a claim without any ability to back it up, simply because it fits with his preconceived theory. That's disingenuous. If he were to say, "It seems to me that", or "What I've seen in my life is...", instead of making a strict claim. A strict claim requires actual evidence and well defined terms, both of which he has none.
Hmm...as to preferences, there are two easy tests:
1. You ask people
When you do, you find that people generally don't like CS. People in developed countries less than in less developed countries. And women less than men, with the gap becoming bigger in more developed countries. And girls less than boys, with the gap becoming larger in more developed countries.
You can also ask them why they choose that way, and in less developed or less prosperous countries, more people say "because of the money". In more prosperous countries, people are, well, more prosperous, so money is less of an issue.
2. You look at how people choose
Same pattern. It's not as if women are forced out of computing and into early childhood education. They choose to go there because, apparently, that is what they want to do.
People barely have any idea about how to hire a software engineer, much less judge someone's true "ability".
Preferences are also very complicated. People may prefer things very differently given the environment. That quote, along with many others, demonstrates the absolute lack of genuineness on the part of Damore.
Damore throws away any pretense of being objective/scientific when he makes claims like this based on metrics that are hardly measurable. A decent scientist would recognize that making claims with very serious implications like this is greatly irresponsible.