Including only the bundled/minified app is possible, leaving no node_modules folder at all - or, at least, just the native binaries needed.
As for bundling the whole Electron runtime on every app: technically it's possible to have a shared runtime - as this 3-year old issue shows, many people have attempted various approaches: https://github.com/electron/electron/issues/673
However, sadly no one has stepped up to come up with a general solution. While there are disadvantages and some reasonable arguments for bundling the exact version of the runtime required by an app, it seems efficent use of resources isn't enough of a priority..