Does {$I Virtualizer_MutateX_Start.inc} always refer to the first virtual machine? Or to any of the defined virtual machines?

It’s not defined to a specific Virtual Machine (but it can be easily changed to be defined for a specific virtual machine). That macro is a bit old and it was created when the different VMs could not be tuned up separately. 

In latest Code Virtualizer, you can define each VM in a different way, so, you can create a complex VM and a lighter VM, and refer to each one using either VM1_START or VM2_START (that's better than using the Virtualizer_MutateX macro)