This is not really possible at the moment. This 3D version is using WebGL in Javascript running as a web-application, while the downloadable binary is implemented in C.
So the C version can use the OpenGL C API. Three.js is a big abstraction layer on top of WebGL, but it's certainly in the realm of possibilities. There are C abstraction layers as well.
Electron apps can work great. I have noticed a general bias against all Electron apps and I think it is because of how poorly Atom performed when it was first released. Virtual Studio Code, and RStudio are shinning examples of a good Electron App.
I've run many other Electron apps - they all suffer from the same problems. Ugly non-native UI, DPI scaling that doesn't quite work right, poor platform integration and massive binaries.
Additionally, with something like this, I'd imagine it would be quite possible to port to a simple Node based system with OpenGL support without the need to embed a browser. Would probably improve performance too due to removed sandboxing.
There's a node-webgl package which provides all of the OpenGL ES features with no need for the web browser part, there's also SDL and GLFW bindings available. While it's not full OpenGL - I couldn't find any well maintained GL bindings at least - it should be completely sufficient to port a WebGL project.
I've searched a lot for such a package, most are five years old and doesn't work. Best I could find was the x11 package, but most examples doesn't work. And if you go with a wrapper you could as well use Electron or nw.js witch I'm using atm.