Basically how this works is you have your MODx core installation, and you can pretty much ignore it. The extras are in themselves mini-applications that work within the core framework; these are what you work with to build and cusomize your site. They all have extensive configuration options, and MODx provides several methods of configuring them. They all also have their own mini-template capabilities for customizing their output.
Wayfinder is a good "snippet" to examine, as it supplies one of the most basic functions of any dynamic website, dynamic nested menu structures. By default, it generates a simple nested unordered list, reflecting the structure of the Resource Tree in the manager. It is also good to examine since it exemplifies the best of "the MODx way" when it comes to development practices.
Of course, as you've already clearly learned, every site is different, and no matter how flexible and customizable any existing extra may be, the time comes when it just doesn't quite do what you want. And there is where MODx really stands out. You can either extend and modify an existing extra that almost does what you want, or develop your own.
I think you would find these examples to be interesting, even if they don't fill a need that you have right now, they are fascinating examples of extreme MODx development and what can be done with MODx by thinking outside the box.
https://forums.modx.com/thread/78039/tutorial-create-seo-ajax-framework-revo-2
https://forums.modx.com/thread/77735/ro-ides-editor-and-framework-for-modx-revolution-2-2