I'm not convinced that the same story will play out for Microsoft. There are so many companies producing x86 and x86_64 machines that to coordinate them all to begin producing ARM machines instead would be a difficult, protracted, and expensive venture. I would expect it to take far longer than Apple's relatively recent transition from PPC to Intel given the number of players in the coordination. I doubt the software vendors will begin producing ARM software en masse until ARM hardware is prevalent, delaying the process even further.
I think we'll end up with multiple, fairly incompatible versions of Windows for each architecture until it's clear whether or not ARM is really going to take hold on the the desktop.