I didn't state the problem is invalid, I merely provided anecdotal evidence from my years of experience in using DPI scaling in Windows to demonstrate that it's a non-issue.
Which is the key factor here. It's not Windows' fault specifically, but it's a problem that occurs when using (very common software on) Windows. To the end user, what's the difference?
If the problem is with Windows, finding acceptable alternative software is unlikely, if it is possible at all. Even worse, users are likely to see the problem affecting most of the applications they use rather than just some specific applications.
I'd say end users would notice and care about the difference between those two scenarios.
You haven't met very many end users, have you?
If Skype and iTunes -- which together are probably installed (one or the other) on a huge percentage of home systems, and a nontrivial number of corporate ones -- are ugly at higher resolutions, then there's a serious problem.
Sure, they shouldn't write shitty software, but it's now Microsoft's problem due to how it impacts the platform as a whole. At least in the case of Skype, one assumes they could fix it (since they now own the product); iTunes is ... probably more complicated.
If people generally spend most of their time in IE/Chrome/Firefox,Word,Excel,PowerPoint... and they all look great and Skype and iTunes look bad, I'd expect people to complain about Skype and iTunes.
If, on the other hand, people spend a lot of their time in applications that look bad I'd expect them to have a broader complaint (which may or may not be about Windows since, by assumption, we are talking about people who don't understand what's going on under-the-covers).
The problem is that both the OS and popular apps need to support it, otherwise in most people's eyes it will seem like Windows is "broken".