The author of that article says "I know from personal experience that today [2005] Microsoft takes application compatibility very seriously". And if you want to install Windows on a computer that already has a Linux distribution installed (dual-boot), then Windows will replace the existing boot manager, making it really difficult to boot Linux. That thing used to happen then, and it still happens now (2015).
Yes, it's annoying, but it's not app compat. And dual-boot is pretty far outside the mainstream, I don't blame them for not building out other boot loader detection and integration. Other bootloaders change frequently, and windows install discs come out maybe every two years. It's better to have consistent behavior (windows install WILL wipe your MBR) than sometimes it works and sometimes it doesn't, and when it does…
It's not that they even try. Not even a little. Last time I installed Windows on real metal, it didn't even warn the other operating system would no longer boot. Microsoft probably has an internal policy to consider installing Windows is an upgrade.