> So I've wondered if the Intel x86 instruction set also has this accident and, thus, can run operating systems that use privileged instructions but not know they are running on a VM. Or maybe the ability to run on a VM was from some extensions to the Intel instruction set. Do you know?
No, originally x86 was very difficult to emulate in a virtual machine. User-mode can be run directly on the processor but, for kernel-level code, binary translation was necessary to dynamically re-write the code containing privileged instructions. However, these days nearly all modern x86 processors now have extra instructions specifically for virtualization.
> Does the Microsoft CLI/CLR software have some security features beyond just any native program
There are a bunch of sandboxing features available in the CLR but most applications run with full trust and can do anything a native program can do.
No, originally x86 was very difficult to emulate in a virtual machine. User-mode can be run directly on the processor but, for kernel-level code, binary translation was necessary to dynamically re-write the code containing privileged instructions. However, these days nearly all modern x86 processors now have extra instructions specifically for virtualization.
> Does the Microsoft CLI/CLR software have some security features beyond just any native program
There are a bunch of sandboxing features available in the CLR but most applications run with full trust and can do anything a native program can do.