Yeah – installing a Site when you’re new to GP can create a bit of confusion.
Sites don’t just install theme settings – but mostly include Customizer > Additional CSS and can include Elements.
And as general rule regarding hierarchy:
1. Customizer settings applies globally.
But as the Themes code is full of hooks – actions and filters you can change most pieces. For example the Blog Options filter:
https://docs.generatepress.com/article/option_generate_blog_settings/
Now you can have a different layout for different archives.
2. Elements
Hooks and Headers are very similar except the latter comes with controls for designing Heros and ( without using filter ) always displays in the same place.
Layout Elements allow you to make changes to some customizer settings. As well as apply Layouts and Disable things.
3. Layout & Disable Element Metaboxes
Both of these are in the post editor allowing you to make changes at a post level.
When it comes to layouts: 3 beats 2 and 2 beats 1…..
Hope that helps