"In other words, it is for new-build infrastructure only, and customers can’t repurpose existing racks to run Azure Stack.
Microsoft’s reasons for doing this are understandable: it can’t guarantee optimal performance unless it can control the hardware Azure Stack is running on..."
The implication of the reason given in the quote above is that Microsoft is going to guarantee optimal performance for this product.
There're a couple of problems with the idea of guaranteeing 'optimal' though, because 'optimal' is a relative concept that only applies to a specified context. For example, the optimal speed, in terms of fuel efficiency, for two, or more, different road vehicles will not be the same. Furthermore, the optimum fuel efficient speed for any one of those vehicles will depend upon its load i.e. whether it is empty, partially-loaded or fully loaded.
Then, whilst it might be possible to quantify the optimum fuel efficient speed for any particular vehicle, for any particular load, how would you go about quantifying 'optimal' performance of software on a particular hardware stack, other than by referencing it to artificial benchmark scores? This being the case, then there's no reason why Microsoft couldn't guarantee 'optimal' performance for its software on any hardware stack.
Finally, a guarantee suggests that Microsoft is actually going to accept both the responsibility and the financial penalties it will incur when a customer decides that the performance it is achieving is not optimal.
So no, I don't buy the idea that Microsoft's imposition of restrictions on hardware is anything to do with performance; simple collusion with the named hardware vendors seems much more plausible.