The main source of incompatibility would be the actual compiled binary for native code (right now only C++) programs. There may also be WinRT APIs that will not be available on ARM, and WinRT applications can also use many regular Win32 APIs, some of which may not be available on ARM.

As far as I know the "app store" is the only distribution option except for a mechansim being talked about for enterprise customers.

Have you worked your way through the blogs yet?

http://blogs.msdn.com/b/b8/