I hate to be critical, and maybe I'm missing something, but this essay didn't read well at all. Sounded like somebody who didn't fully understand what they were doing thrashing around.
We use anchor tags as buttons any more because clicking on buttons should (eventually) change the href.location. That means, yes, right-click should work just fine, opening up a new window with your action applied to the current state. Don't look at buttons like Javascript events. Rather look at them like code that changes the URI that then kicks off Javascript events. It's a subtle difference, but it's very important. An anchor as a button isn't the same as a button because they're two completely different things. Your mental model of each should be different.
I don't see where there's much of a mystery or rant here, but maybe I missed it.
It really just depends on the context: In a web app (the example in the essay) or Chrome extension, traditional navigation mostly falls away, leaving something almost entirely controlled by JavaScript. Buttons and links have two distinct styles and places to be used, but in a web app they usually functionally do the same thing. In Bootstrap, the issue was how to make links that look like buttons also behave like buttons, which all the issues still apply to.
Once someone brought up the keyboard issue in my pull request, I researched for a while, and then made the post once I angrily realized the full extent of the problem.
We use anchor tags as buttons any more because clicking on buttons should (eventually) change the href.location. That means, yes, right-click should work just fine, opening up a new window with your action applied to the current state. Don't look at buttons like Javascript events. Rather look at them like code that changes the URI that then kicks off Javascript events. It's a subtle difference, but it's very important. An anchor as a button isn't the same as a button because they're two completely different things. Your mental model of each should be different.
I don't see where there's much of a mystery or rant here, but maybe I missed it.