This is a great example of persuasive, but superficial, analysis.
1) It may well be a dumb thing they do, but is this really "why big companies keep failing?" There's no real examination of this causal assertion which seems central.
2) Is it really the "stack"? That is to say, do people really assume that just the layer above them is trivial? I see engineers all the time assume that basically everything they don't understand is trivial. For example Elon Musk's famous assertion that the hyperloop is "Basically just like an air hockey table. It's not that hard". Well in turns out air hockey pucks don't need to transport people, g-forces aren't important for air hockey versus not murdering your passengers is quite important for a public transport system. Air hockey pucks don't need to breathe versus people do which makes the vacuum part quite critical and challenging especially since you have to figure out how to get people in and out without rupture. To think of it as like air hockey you are assuming that all interesting/challenging parts of the problem are trivial. To be clear: I think that this hubris is basically essential for innovation. I really don't think people would ever innovate if they worried too much about every small detail of things, but this is why a large proportion of experiments by everyone (big and small companies alike) fail. I don't think the layer above you in the stack is the important part here and the article doesn't examine whether that characteristic is important.
I think you are criticizing an idea for not being a study. I think it's a reasonable and interesting idea, but at most it is something to consider, not some infallible axiom. More akin to "the Peter Principle" than a theorem.
Point 2 is... neither important nor really germane. (I don't care what engineers say, and Musk isn't an engineer anyway.) The point is that people understand their customer bases, and sell to them, and then imagine that means they understand how to succeed in the business their customers are in, and... not so.
It's basically a reminder that understanding the customer is everything. No matter how good the tech is, if you don't solve the customer's problem... they aren't buying.
Your point 2 is interesting, but Musk isn’t any type of engineer really, just a money guy that uses engineer words. It seems more likely that he assumes a Hyperloop would be trivial not because it is a simple application of some lower framework that he’s got a deep understanding of, but because he hasn’t been given an itemized bill for one.