The problem with the article is that it's two arguments pretending to be one.
The first argument is about people. People romanticize the flaws of their tools, turn vim macros into a personality, and mistake the feeling of cleverness for output. Fine. True. Bill is correct that a lot of tool evangelism is tribal signaling dressed up as productivity advice. However, people join these tribes because they get benefit from it. If the tool wasn't meeting their perceived needs, they wouldn't be passionate.
The second argument, the one in the title, is about tools: that being invisible is what makes a tool good. That one is fundamentally wrong, IMO.
Halfway through, Bill admits the invisibility test "is a personal one." Which means: a tool is good when it disappears for you. Sublime is invisible to him because he's been at it for fifteen years. On day one it was not invisible to anyone. In fact, I remember buying a book and reading it back in the day about how to get better at using Sublime. So "good tools are invisible" reduces to "good tools are tools you've already mastered." That's not a claim about tools; rather, it's a claim about experience. Every powerful tool is bad to the novice and invisible to the expert. So I'll categorize this one as a veiled tautology.
Then there's the metric. Bill's "honest test" is wall-clock time and mistakes made. Anyone who's less familiar with a tool is going to make more mistakes up front. I have a couple of professional-grade sanders that I've used for some projects around the house, and because I use them infrequently, I tend to make mistakes when I get started since it's not my core competency.
The right question for a power tool isn't how fast you did the routine thing, it's what became possible that wasn't before. Git is not invisible to anyone, ever, and it's the most successful version control system ever built, for better or worse. Of course, lots of people also think Git is bad, so I'm not making any particular claims on that front, but it did manage to reach a local maxima that led people to jump ship from SVN et al. SQL has been the standard for fifty years and is famously brutal to master. A profiler demands your full attention every time you open it. These tools are good because they expand the frontier of what you can express. A tool that makes the impossible merely hard beats a tool that makes the easy invisible. Bill's metric scores the median task and is blind to the edge, which IME is where I end up spending more of my time as I grow as a software developer..
The configurability section is where the essay argues against itself. Bill's fix for "highly configurable" cop-outs is "good defaults, plus escape hatches for the rare cases." But the escape hatch is the whole problem with his thesis. The moment a tool has escape hatches, the knowledge to use them is valuable, and the tool isn't invisible even to him. He wants the power and wants to disown the learning it costs. You don't get to do that. The escape hatch and the learning curve that leads to it are the same object. He even admits it. In the learning-curve section he concedes a steep curve "could absolutely be a cost worth paying" if the payoff is real productivity. That's the entire counter-thesis. So I'm not really sure what point he's actually trying to make with this article besides that you should have good defaults for tools.