When your programs are running on a VM, the linux that loads and runs your binaries is not at the bottom; that linux image runs inside a virtual machine which i

When your programs are running on a VM, the linux that loads and runs your binaries is not at the bottom; that linux image runs inside a virtual machine which is constructed and supervised by a hypervisor which sits underneath it all. That hypervisor may run on the bare machine (or what passes for a bare machine what with all the sub-ring-zero crud out there), or may run on top of another OS which could be linux or something else. And even if there is linux in the middle and linux at the bottom they could be completely different versions of linux from releases made years apart.