To be able to upgrade NumberNine easily, it's nothing more than a Symfony bundle. That means that your app will be a project based on
symfony/website-skeleton with a clean folder structure to start with.
NumberNine automatically configures everything in the background, without altering your own configuration files. You can at anytime override any setting like you usually do with Symfony.
Symfony's documentation is 100% valid for NumberNine, although you don't need to touch the security config unless you have a very specific need for it. NumberNine already creates the user management layer so you don't have to go through all steps.
NumberNine makes extensive use of Symfony's event dispatcher to allow extending its features from your own code without having to modify the core code.
You'll be able to add or modify user capabilities, route templates, custom post types, and much more.
In a classic Symfony application, a page is rendered with a single controller and a single template. It's fine, but hardly reusable.
In NumberNine, you can create components and shortcodes that will handle a small region of your page with an isolated controller and a specific template for this region, with virtually no performance impact.
You don't have to code your app "the NumberNine way", as there's no "NumberNine way". You're free to code like you usually would code with Symfony, creating pages aside from the CMS and using your own Symfony routes.
Upgrades are done with
composer update. If there's a new version of any of NumberNine's packages, your project will be upgraded.