The only issues would be in ChakraCore were to support additional ES6/7 features that people started to use that wouldn't work on a V8 node.js instance, or the other way around.
Suppose you could transpile what is possible, then throw errors otherwise, however that would involve parsing each file in an NPM module which is probably an unreasonable task performance wise.
It's easy to install NodeJS 5 with v8, it is however unacceptable to be required to switch to Windows.
This could change if they get around to porting it completely. For now the only thing they've committed to in the next 6 months is porting the ChakraCore interpreter(but not the JIT).
Edit: even if they had waited until the JITless builds for OS X and Linux were ready I'd be happier. This definitely feels like jumping the gun.
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.