On your last point about the system cannot be fixed, and it could be a lot worse - everything else you're citing is certainly a problem as well. Maybe even bigger in some cases. I still don't see how those are responses to this article's points. It's kinda like a version of "whataboutism" that you're proposing.
I just don't really get the casualness towards a problem that is widely regarded, among scientists, as something fairly serious - "publish or perish". Why do a handful of publishing houses get to have so much control over the careers of people who dedicate their lives to a field, often at great personal and financial expense (in the form of lost wages and consistently lower pay)?
I thought science was supposed to be about the discovery, and dissemination of information. Why is the process of doing capital-S Science so gatekept behind university or big corp doors? Why is the only output of most scientific research a dozen pages of virtually indecipherable material? Why can't we know about the process that was taken to arrive at those conclusions, especially when they are so incredibly consequential to all of our lives? Science is responsible for virtually all modern advances - why doesn't the public have the right to understand it fully?
That's my takeaway from the article, and I'm curious how you arrived at such a wildly different conclusion.