As long as each JS engine uses the same API (at this point V8's C++ API, hopefully something engine neutral later) what difference does it make?
Node is a large code base. The Chakra merge will eventually work and pass all tests - give it some time. One cannot reasonably expect such a large merge to work flawlessly out of the gate. Even the IBM PowerPC port of the V8 engine took many months to stabilize - and it's the same v8 engine.