Sure, the anti-Microsoft side of the AARD story has been long-spoken, but have we heard the Microsoft side? Basically, "Yes, we admit it. We deliberately locked out DR-DOS, and we don't have to apologize for doing it. Windows was designed to run on MS-DOS or a 99.9% clone, and DR-DOS just isn't good enough because it's only a 90% clone." http://blogs.msdn.com/larryosterman/archive/2004/08/12/213681.aspx

There's a bit of corroborating evidence for the Microsoft viewpoint, but the history is short enough that this will always remain a philosophical argument that can never really be proven one way or another. Basically, Windows worked just fine on IBM PC-DOS. Up until PC-DOS 5, it was identical to MS-DOS except for the two bootloader files. However, in version 6 IBM parted ways with Microsoft and developed PC-DOS on its own. So if Microsoft wanted to, it could've sniffed for PC-DOS and refused to run Windows 3.1 on it. But this didn't happen.