Microsoft and NVidia have a history of collaborating to adapt Windows APIs to NVidia hardware. DirectX 10 was practically designed to NVidia's next-gen hardware spec.
If Microsoft is serious about ARM, there's no reason they couldn't work together to ensure the CPU is optimized for Microsoft's emulation layer.
In general Microsoft are in favour of doing anything that sells more copies of Windows and I have no doubt supporting an extremely fast Nvidia CPU on ARM is possible. It might never run software as well as x86 but maybe if it ends up being faster for games (which could be possible with MS and NVDA support) then people will buy it.
If Microsoft is serious about ARM, there's no reason they couldn't work together to ensure the CPU is optimized for Microsoft's emulation layer.