ARM Windows won’t include an x86 emulator, and as such will not be able to run existing Windows programs. It is, however, the same operating system with the same APIs, meaning that it should be possible to recompile existing software and device drivers for ARM Windows with few difficulties. The same applications should, therefore, become available on both platforms, as should access to the same hardware.
So, as soon as they’re (nearly) done transitioning their user base from 32-bit -> 64-bit OS, drivers and apps, Microsoft is going to force another bifurcation, but for what benefit? The advantages of running on ARM will likely be negated by background Windows processes.
Or, maybe they’re banking on ARM Windows 8 taking a sufficient amount of time to come to market that they’ll be able to get “all day” battery life on their tablets. Meanwhile, your iPad will last all week under full use.
Update 5:41pm: Apple has avoided issues like this in their architecture switches (most recently, PPC -> x86) by allowing for Universal Binary applications, containing the code for both architectures all in one App bundle. For the sake of their users, Microsoft should implement this. Or perhaps they’re expecting everyone to buy Office 2012 ARM edition for their tablets and a separate x86 edition for their laptops and desktops.