Block layout
As documented at Site layout & Menus by default the site header and footer are built by the frontend. That means, the Drupal Blocks Layout configuration is ignored for custom-elements rendered pages.
However, with the optional "Lupus Decoupled Blocks" sub-module the configured blocks may be rendered and included with the page response. This may be useful when Drupal should generate the content for a certain region for every page, e.g. a sitebar.
How does it work
When the module "Lupus Decoupled Blocks" is enabled, all configured blocks are rendered with custom elements for every page. The result is grouped by region and added to the custom-elements page API response under a new top-level blocks key. In turn, the frontend just needs to render and place the custom-element content of each region on the page.
Site Templates
Drupal CMS supports site templates: pre-configured starting points that combine Drupal recipes, a theme, design elements, and default content into a fully functional website ready to use from day one. See the Drupal blog post on site templates for the broader vision.
Debugging API requests
For debugging API requests and responses, Lupus Decoupled Drupal offers integration with REST Log module.