In the real world, if someone exploits your PDF reader, they don't have to circumvent your OS: your OS hands over everything you can access, by design. One could argue that a better security model baked into the OS would make more sense than a virtualization hack, but the latter has the advantage of actually existing.
Any attempt to use anything else leads to termination.
The system administrator at installation time.
> What defines which resources they are given?
Applications just have a request list of what they require.
If the administrator doesn't allow them for the given application modules (executable, dynamic library, function call,...), bad luck.