Microsoft weren't hired by Id to port Doom. They did so exclusively for their own purposes: to show off Windows 95 with DirectX as a performance gaming platform. They licensed the Doom engine, made their own changes, and released Doom 95 usable with a retail copy of the game assets.

Oddly enough, the project of "porting Doom to Windows" was started by Gabe Newell, who worked at Microsoft at the time,