Strawman. I said nothing of the sort. I'm taking the article at face value. The article reports that regularly, stores of your chain are understocked that much that you are losing money and customer loyalty. It is not saying those are special rare issues.
Now, there are two options: The article is wrong, or it is right. If it is wrong, then you need to change nothing internally. Customers will see in their nearest store that the stock is alright, some might even come out in support, a small welcome challenge for PR. But looking at this thread, at the comments not being a discussion about journalistic objectivity below your top-comment, there is some support for the thesis of the article. If the article is right, the system needs to be changed if you want to compete with the other stores that actually succeed in stocking the items customers came to the shop for. In that case, the impression I would get from the attitude you are reflecting here (and which according to the article is the one of management) is that parts of WF are burying the head in the sand, which would likely be disastrous for your company.
It is easy to optimize for the wrong metrics, especially big corporations. Short term shareholder value, cost reductions - cost reductions were echoed by management in the article as motivation for the OTS system. Combine that with a good portion of institutional inertia and wrongly placed respect for authority, and this is how companies die. Which, again, might not be at all what is happening here (and Amazon and stuff, I know). It just looks like an example of it, which I think is interesting.
The article is wrong about the regularity of the issue, the "weird control systems" (not sure what connection you're seeing with employee protection laws), and the causes.
But you misunderstand me if you think I'm burying my head in the sand. I don't deny that Whole Foods has issues with its ordering processes. In fact, I think the company has been going in the wrong direction there for a long time. The article is just so, so off-base - originally I didn't intend to argue with it, but now I've become this guy: https://xkcd.com/386/
It will be interesting to see if Amazon can improve the situation through automation. Generally I've seen stores that use automated ordering systems be far worse with their out-of-stocks (Kroger, for instance).
But it actually is meant for things on regular shelves, it doesn't apply to the produce department, which is what all the pictures in this terrible article show. It also doesn't apply if the product is going to be out-of-stock for a known period of time. It's meant for situations where the buyer didn't order enough and it will only be out for a day or two.