I couldn't agree more. Not to bash on this project, what is the point here exactly? Godot has an excellent build system(scons), plugin system with scripts(GDScript) and even native plugins with C++. And a bunch of tools that are super useful for development. Like you said, "wrapping it" inside NodeJS is just asking for trouble and might be a maintenance nightmare.

For context: I have been playing with Godot custom C++ modules in the past year and I've had a blast. Such as a wonderful project.