The problem in Windows' case is that there never was a clear specification regarding what kinds of files should go where. The directory structure and environment in every version of Windows is a little different, and it's hard to write an app (or an installer) that does the right thing on all of them.
I think the combination of complexity and obscurity of those two links reinforces my point more than it refutes it. There's a reason why basically no one gets this stuff 100% right, including some of Microsoft's own first-party applications.
