"I'm no security expert, but this article, and the FastCo article about NASA programmers suggest, at least to me, that computer security is a problem that emerges from incompetence in using tools and designing programs."
While true that accounts for a large amount of the problem, probably the clear majority, computer security would remain a problem even if developers were uniformly highly competent. Competent use of existing crypto systems, which are broken three or four years later, would still be a problem. Meltdown and spectre would still be a problem. Building a safe execution sandbox is legitimately difficult.
But it would be a qualitatively different world than the one we live in.
Certification solutions to the software problem generally face the problem that it is very difficult to imagine any scenario other than one in which people grotesquely incompetent to write the certification rules are the ones writing them. We do not, for instance, want our certification authority to sit there and mandate waterfall design processes, which I would consider at least a 25%-probable outcome, and that's awfully large for something as catastrophic as that would be.
"WRT the house analogy, it's easy to extend that to "intelligent" attackers: intruders of any kind, e.g. robbers, animals, etc."
No, houses are never under such intelligent attack. Even when attacked by humans, they are not attacked by ninja stealth thieves who go in, photocopy your SS card, and get out again without leaving a trace or something that sounds absurd to even use as an example. There's no physical equivalent to breaking into millions of houses at a time and making off with such data. They're attacked by people who smash through the physical security. Anybody can do it. "Anybody" is who does it... above-average IQ people are not generally breaking into houses. (Above-average IQ criminals find much more lucrative and safe criminal hobbies.) Not just anybody can put a tap on a fiber optic line, feed it to a high speed data center, and process it in real time to extract out terrorism threat info, or even just exploit an XSS vulnerability on a website.