Not everyone. Some are very successful with it. The problem is that everybody wants to copy that success and tries to cargo cult themselves through it without understanding it.
"let’s stop pretending Agile was some sort of cure all."
That's certainly good advice. Agile is more of an attitude than a solution, and attitude is not going to solve all your problems. Even if you are as Agile as you can be, you still need to solve your problems. It's just that being Agile might make you more flexible and effective at solving those problems.
And Lean is certainly more comprehensive than Agile. And I don't think they contradict each other. In fact, they're very similar; they're both about empowering the people who are doing the actual work.
"management thinks the focus should still be scope and deadlines and efficiency, ignoring that the deadlines are arbitrary and the requested time estimates are a form of waste."
Then management is not Agile and hasn't properly learned what it is. That is sadly common. Agile is not magically going to solve bad management, but Agile does emphasize keeping management at a distance and empowering developers.
"Agile actually tends to mask the core problem, which is a systemic, bidirectional lack of vertical trust."
Does it mask that? I think it exposes it. Without that trust, Agile cannot work. Agile insists on that trust. I suspect that every case of broken Agile is caused by a lack of trust. Fix the lack of trust (or use a system that works without trust if you absolutely must).
"Did you know story points were actually invented to obscure time and help alleviate this problem? That backfired too, didn’t it?"
Yes I did and no it didn't. Every single team I've worked in over the past 6 years knew this and kept repeating it every time someone comes along and tries to match story points to actual hours.
This first half of the article suggests the author has mostly worked in very toxic management cultures.