I strongly upvoted this post because I believe epistemic empathy is important.
The word “irrational” has too many meanings, and I try to avoid it. And I try to direct criticism at arguments rather than people. But I do want to answer your final question as best I can. I’ll just phrase it as problems with arguments rather than people’s irrationality.
In my experience, the problem with arguments against COVID-19 vaccines is that they mainly consist of evidence that there’s risk involved in getting vaccinated. To usefully argue against getting vaccinated, one needs evidence not only that vaccine risks exist, but that they’re worse risks than those of remaining unvaccinated.
Similarly, arguments against masks are usually arguing against the wrong statement. They argue against “Masks always prevent transmission”, when to be useful, they should be arguing against “Masks reduce transmission”.
Good points are made in other comments about the significance of weakest bonds, but mostly I want to say that I like this post because it’s making a clear point with clear reasoning, and was very readable.