The point is that it is a mistake to take a methodology that was created for incremental process enhancement along a manufacturing line and apply it to software development.
I look at a book like The Phoenix Project, written by some fairly respected software industry folks like Gene Kim, and they also recommend the opposite: that software development and IT operations actually are a lot like an industrial shop floor and benefit from being organized in an end-to-end pull flow like Kanban.
I look at Four Steps to the Epiphany by Steve Blank, or Lean Startup by Eric Ries, while they aren't specifically dictating a Kanban board in their work, they're clearly philosophically in the camp of a pull-based approach to organizing work and limiting work-in-progress.
So, what I haven't determined from your article is, what specifically is flawed with these authors views and my experiences? Am I being over-broad in their inclusion? My interprtation of your article this far is a well-meaning but under-argued philosophical aversion to being lumped in with other industrial engineering practices.
Edit: clarity
I've seen companies/projects with all of those things still fail because of a poor process. This is where something like Kanban can help, IMO. Not trivial to implement though.
This isn't really a criticism on the point your making in the article by the way, which I think is still valid. I find it weird too that software development is being shoehorned into a manufacturing job control system.
Kanban/lean is a pretty simple idea (not always easy to execute): eliminate waste in your work by smoothing the flow of requirements/changes. This treats your end-to-end delivery capability as a syatem and one that should not be overburdened.
The clearest sign of being overburdened is when you have a lot of work in progress but nothing to show for it. So instead of a genius PM/business analyst/product owner handling out a tome of requirwments from on high with a thud, you break the work down into a minimally useful / marketable chunks, minimize work in progress, deliver according to some priority, and iterate and learn from the results.
This is the philsophical foundation of lean Startups (customer development), lean development, and much of the work on Devops.
So the article rails against Kanban ... And almost seems like its advocating for the same thing with its goal-driven approach to delivery (?).
Any methodology or process framework is subject to misinterpretation or abuse. This is why "agile" and "scrum" are dirty words to many - it's hard to tell what you're getting, as the term has been twisted to suit vested interests. It looks like it is Lean and Kanban's turn to be trashed due to ersatz versions being forced on teams.
But articles like this aren't helpful unless they explain what they mean Kanban, and what aspects are ineffective - clichés like "software is different" don't illuminate.