In other words, WOA is capable of running desktop apps, but that will not be allowed except for the blessed applications, which currently only include Office. Just like the Windows Phone situation. It is an interesting/ballsy strategy, very Apple-ish, sure to upset a bunch of people. But it is probably the right decision, and will work out well for ARM tablets. It does make for some awkward situations around the Intel/ARM boundary.
I am curious why they would bother to support the Desktop Experience (Explorer, IE desktop, etc.) on ARM if it's only there to run Office. Seems pointless, but maybe it was just the easiest path.
There have been lots of hints about some support for native code on Windows Phone coming. I would seem obvious now that the native support will be in the form of writing WinRT apps -- exactly the same as for ARM tablets.