1. A computer-implemented method of optimizing across a protection domain boundary in a system virtual machine, the method comprising: identifying a program call from a first protection domain to a second protection domain; augmenting a first region node of an intermediate representation of code comprising a source of the program call with information configured to identify the first protection domain; augmenting a second region node of an intermediate representation of code comprising a destination of the program call with information configured to identify the second protection domain; inlining the first region node and the second region node to optimize the program call; and emitting native instructions for executing the optimized program call within one or more corresponding protection domains, wherein each instruction in the native instructions comprises a field that references or directly encodes protection domain information for the instruction; wherein, upon executing the instructions, the instructions are executed with the privilege levels identified in the corresponding protection domain information without altering a privilege level set in a hardware processor.