In any case, people are focusing on a minor detail rather than the interesting piece of this: The point is, when you buy from the Microsoft Store, you can get that's set up to have a "best-effort" configuration of Windows--one where the choices of what to install and what not install are made from the perspective of making the customer experience great, not based on who paid the most money.
If you want the same thing done to a PC purchased elsewhere, perhaps you have to buy a copy of Windows (I work for MS but I have no idea whether that is the case or not). On the other hand, all of this setup/optimization is free, so it's quite likely cheaper to pay for Windows a second time than to pay, say, Geek Squad for their questionable "PC optimization service."
If the store just said "come in and get your PC optimized for $99" I'm sure no one would have an issue with it.