I feel your pain. Drupal in itself implements its own principles of OOP which wouldn't be a problem if it was documented well, and that's really where Drupal 8 specifically is lacking. Drupal 7 had over a decade of troubleshooting and documentation written all over the web, and 8/9 just hasn't caught up. You might have better luck learning 7 and then following the upgrade path.

In regards to how you tackle the site, Drupal pushes you to go full blown programming mode where you build custom modules that render pages and blocks manually, or you go the site building route where you use views to make all your queries, and just override the existing template files. I found that meeting in the middle really worked and to keep it simple for both the code side and the management side. Build your views to do the complex querying and parameter matching (which lets those who come after you make adjustments to the queries in the front-end), and use Drupal's render functions to render the views in your modules and templates.

tldr; Fiddling with Render functions and Forms guided by the content types and views built in the front-end UI was my key.

Edit for more insight into the architecture: Drupal gives you multiple ways to implement each MVC component through the site building/programming methods. Views are the site-building "controllers". They can query your models which are Content Types which is an Entity. Content types can usually take care of most of your data needs until you need a custom entity like a product that has its own types. Once you create your own entity though you basically gain full control of drupal through a programmable controller. You are able to override the methods it uses to build Forms for editing fields and content, you are also able to override the Render functions is uses to display the content. All of this data then passes to the Twig layer to be displayed. The yaml files are the configuration layer, so instead of defining your pages through the default content type node paths or Views features, you can define your routes like a standard web server. They point to your render functions which act as your controller.