There's a difference between "red flags" and "imperfections". Every team has faults, which if you're experienced at interviewing/working many places, are usually pretty easy to figure out. These are distinct from "red flags".

Early in your career it can be hard to distinguish the two, but once you've joined a company where there really were "red flags" you quickly learn to differentiate.

Many people are reading the author's interview uncharitably as simply misunderstanding how to answer non-technical question, but I have absolutely been through loops (thankfully rare ones) that did have a "let's press on sensitive issues and see how tough this candidate is" round (one place brought in a consultant who bragged about his experience working with hardened criminals and terrorists to build out a true psych profile on candidates, I declined after learning he had had some "trouble" at a previous high profile job)

Sounds like you've never worked for a truly toxic org, which is great. But, especially if you're interviewing with smaller startups (as the author mentioned), there is a lot more variance and some truly messed up teams (and some truly remarkable ones as well) out there. I've noticed that HN increasingly doesn't have people that work at startups any more, so many people are probably less familiar with what's out there.