Yes. Nwjs is just a Chrome wrapper for your project in executable form. Basically you're bundling chrome with your game, and when you run it out opens a standalone version of chrome to load your game with, so it's basically no different than running it off a webpage.
Yes that's what I mean by unified. The level of security pretty much depends entirely on how you design it. If the data files are located on the host computer, the peers would only be able to access them if you wanted them to be able to.
The server... Is literally just like the computer you are using at home. You'll need an operating system like windows or linux, download chrome, and run it in a desktop environment. You can use VNC to control it remotely.
If your server is command line only, you won't be able to run your project. You'll want one that can run (or virtualize) a windows or linux desktop. Technically MacOS would work too but... I don't think anyone does that.