There is not much to understand in a node_modules folder, it just contains the dependencies you included in your package.json file (and their dependencies, and the dependencies of their dependencies, etc.).
ThreeJS can be used for many things, a one-size-fits-all starter may be hard to find, it could help if you would precise what you expect to build with it. If its just for learning purpose, you might as well build your own boilerplate.
Mugen87’s starter uses Rollup, which is what Vite uses for production build, so you’re not so far from it in the end. You could also fork his repository to make your Vite version.