OK then, I guess the safest path for those who intend to use Cocos Creator is just use Cocos Creator to create a new project and stick to it. I don't check the latest version but according to forum posts Cocos2d-x-lite tends to be an older version than the latest Cocos2d-x, I hope it's decoupled from Cocos Creator at some point as an independent module with some basic dependency checks.
By designing 3D from scratch, do you mean deprecating the current 3D API in Cocos2d-x?
Another concern is about Android Studio, is it possible to build what Cocos Creator produces with Android Studio? It's important for debugging on Android and using third-party Android SDKs that expect gradle build.