I've got some good news! It already is a generic 3D level editor. It comes with some assets I made, but those are mainly for demonstration purposes. You are meant to replace the files in the assets folder with whatever you need for your game.
The shapes can be rotated on yaw and pitch (X and Y). Otherwise, you can add or modify the shapes using your preferred 3D modelling tool; they are all just .obj files in the assets folder. There are some more details in the instructions.html file.