I definitely appreciate that being a C and C++ developer, but you're sorely misled if you think that runtime carries over. Emscripten just translates the language to something usable through asm.js with a similar execution flow, but you end up running JavaScript. That's what it compiles to. Even WebAssembly is designed to run something that is consumed by the very same JavaScript runtime.
Yeah, it's designed to pass through the same mechanisms that handle JavaScript. It's a new byte code standard afaik, too, but one that's used in those systems.
