The code generator is indeed different, the runtime is still Mono.
Mono today has two code generators: Mono's built it one, and an LLVM one. Both generate code after Mono loads and processes the assembly.
Unity developed a different front end to the runtime that does the compilation from IL to C++, the result still requires the Mono runtime to provide services at execution time.
They are currently upgrading their Runtime and are making a version with all the greatest features available coming.
