The CLI is just a command line interface that makes scaffolding and generating a project a lot easier. Adding new components, routes, services, etc... can be done with simple commands. Angular seed gives you a skeleton that you can start your app with, and the quick start provides a super barebones starting point with just a single AppComponent if I'm not mistaken.
I personally enjoy using the CLI and haven't tried the seed myself. If you're interested in how I set up this app, I wrote a blog post (http://houssein.me/angular2-hacker-news) detailing each and every step using the CLI so I hope it helps :) (this was done a few months ago so the progressive elements such as the Service Worker and manifest isn't included)