I was around when the agile manifesto was drafted. It wasn't about eliminating hierarchy in organizations. That's something that started happening later, around and after 2010. The agile manifesto was singularly focused at helping people see how to deliver software without leaning on the old waterfall methodologies.
You must have worked in some very unhealthy teams where psychological safety wasn't present. I'm sorry that happened. But don't confuse your experiences with that of everyone else's. There are lots of teams that are agile from the top down, including those that happen to hold a title with VP in the name.
Don't distract. I'm genuinely trying to help us figure out how to build quality software, using AI, while avoiding all the problems we're seeing on so many teams.
Before the Enlightenment, what we now call science was alchemy. Productive, sometimes brilliant, but without a formalized process for distinguishing real understanding from convincing error. The scientific method changed that, and science became possible.
Software engineering today is closer to software alchemy. We build through craft and intuition, and when it works we often can't fully explain why.
AI is making the labor of producing software cheap while leaving the work of understanding it hard, and that combination is new.
We've never had to build a shared mental model of a software solution deliberately. It has always come for free through the raw effort of writing code.