Windows Notification Services can only communicate with Windows 8 devices (via WinRT). Do you want to send a notification to the user of MVC web app (in his browser) or to your backend - i.e. the MVC application itself?
1. It runs in the 'middle-tier' which we call the mobile service, not SQL azure. You can find out more about how we built Mobile Services and it's architecture on the next Web Camps TV (https://channel9.msdn.com/shows/Web+Camps+TV/)
3. The script executes in-process in the middle tier. It gets invoked, erm, directly! No inter-process-communication necessary to execute a script, only to get to the DB.
4. Yes, your Mobile Service runtime is isolated from other service runtimes. I'll talk more about this in the next edition of Web Camps TV too. To cut a long story short, we run on the same infrastructure offered by Azure Web Sites.