Well, I am not meaning to defend MS, we all have our issues with any OS, but...
MS did design the software, and for whatever reasons, designed it the way they did. Now that it is what it is, they can also say they know what's the best way to use it, as they designed it. Obviously the question is "why did you design it that way in the 1st place?".
We will never know, our choice is to use it, or not. Now that we are using it, all we can do is make it work the best for us as we can. We all wonder why they changed something that worked so well for us, but at the same time, other changes they made were improvements, so it can be a wash.
Their design obviously needs to put at least some program data on C:\ along with the OS, so it is something that we have to put up with if we use Windows. It doesn't help you in this situation, but it is what it is