Now instead of one layer with hardware contact, you have two (assuming you want performance too). Twice the attack surface.
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.