QUESTION: How to keep default sections in the canvas without the possibility to be removed by the user?

By default all components are removable, so that's already covered. In terms of not allowing certain components to be removed, you can take a look at the component api:https://grapesjs.com/docs/api/component.html#component

You would need to set 'removable':false for your three containers.

editor.DomComponents.addType('Header', {
	model: {
		defaults: {
			tagName: 'div',
                        // Component won't be removable
                       removable:false
		}
	},
	view: {
		tagName: 'div',
		onRender() {

		}
	}
});

Adding components during initialization:

const requiredComps = [{
 type: 'Header',
...
},{
 type: 'Body',
...
},{
 type: 'Footer',
...
}];
const editor = grapesjs.init({
   components: requiredComps
});

Another approach: If you are creating a new 'PDF' always add those three components https://grapesjs.com/docs/api/editor.html#setcomponents

editor.setComponents([{
 type: 'Header',
...
},{
 type: 'Body',
...
},{
 type: 'Footer',
...
}]);

If you have an event for creating a new pdf in your custom app that's a good way to attach this logic, if not you could add this logic after the editor is loaded and you could check for an 'empty' project. Events:https://grapesjs.com/docs/api/editor.html#available-events

// Run after the editor is laoded
editor.on('load', (some, argument) => {
   // There are no components(empty PDF), so add the necessary containers
   if(editor.getComponents().models.length === 0){
         editor.setComponents({
              type: 'Header',
              ...
          },{
              type: 'Body',
              ...
          },{
              type: 'Footer',
              ...
         });
   }
});

By default all components are removable, so that's already covered. In terms of not allowing certain components to be removed, you can take a look at the component api:https://grapesjs.com/docs/api/component.html#component

You would need to set 'removable':false for your three containers.

editor.DomComponents.addType('Header', {
	model: {
		defaults: {
			tagName: 'div',
                        // Component won't be removable
                       removable:false
		}
	},
	view: {
		tagName: 'div',
		onRender() {

		}
	}
});

Adding components during initialization:

const requiredComps = [{
 type: 'Header',
...
},{
 type: 'Body',
...
},{
 type: 'Footer',
...
}];
const editor = grapesjs.init({
   components: requiredComps
});

Another approach: If you are creating a new 'PDF' always add those three components https://grapesjs.com/docs/api/editor.html#setcomponents

editor.setComponents([{
 type: 'Header',
...
},{
 type: 'Body',
...
},{
 type: 'Footer',
...
}]);

If you have an event for creating a new pdf in your custom app that's a good way to attach this logic, if not you could add this logic after the editor is loaded and you could check for an 'empty' project. Events:https://grapesjs.com/docs/api/editor.html#available-events

// Run after the editor is laoded
editor.on('load', (some, argument) => {
   // There are no components(empty PDF), so add the necessary containers
   if(editor.getComponents().models.length === 0){
         editor.setComponents({
              type: 'Header',
              ...
          },{
              type: 'Body',
              ...
          },{
              type: 'Footer',
              ...
         });
   }
});

It works like a magic! Thanks for your help @MartinPutz ! I'm really appreciate it.