Love the idea of shipping something smaller. In your proposed idea, would a user still need to make sure node and express were installed? Or can you have a user download a project folder and initiate the same way they would a typical executable?
When developing locally I presume it would be very similar to an Electron project, with npm dependencies for express / fastify on the "backend" side and React or whatever you need for the "frontend" side.
During build, you'd produce 2 bundles (frontend and backend) that tree-shake, etc. such that all js dependencies are optimized together. The frontend bundle should load in any browser (it'd be just a normal website with the only difference being that all REST calls go to /localhost). The backend bundle + any native modules will be loaded in the embedded node runtime so they can be distributed as loose files or packaged in something like Electron's asar.
There, I designed the whole thing, now someone go build it :)