One difference is to be able to ditch Javascript and use a native language(Swift is the first one) to talk directly to webkit.
The other difference is that the apps are "managed" as Chrome manages the renderer process, so in the end you have one manager process and one service process for each app and many process for the UI apps.
The problem with Electron is that for each app, it will need many processes, and if you have more than one Electron app running, it will eat all the resources.
With the architecture proposed, it will be more light as there will be just one instance of the manager processes, and unlike Electron they would not be isolated as they are all centrally managed, also the fact that it wont need to use JS, will also put less pressure on memory resources.
It also uses RPC so that every app have a API that can be callable by others. This in turn can make it form a "network of apps" where the applications can consume the apis of the other apps installed. The RPC service is local first, but can fetch things in the "cloud" if the application needs to.
For me this is my take on what "Web 3.0" should look like.
I have a 0.1 version here and i'm just finishing the final touches before launching it..
Edit: Also i forgot to mention that the distribution of the application and resources(database and files) is over torrent with DHT routing, so you can share a unique address and serve your own applications over internet without depending on domains or a third-party hosting it for you.