### Godot version

v4.0.beta10.official [d0398f62f]

### System information

Xubuntu 22.04

### Issue description

When a glTF file includes a mesh nested under another mesh (for example linking one object to another in Blender), only the meshes on the root level are properly imported to the generated scene.

![imagen](https://user-images.githubusercontent.com/172656/209988973-f4963ef7-aa57-4774-a495-8623a446f32e.png)

In the image you can see the same `.glb` file imported using drag and drop (on the left) vs using `GLTFDocument.generate_scene` (on the right)

### Steps to reproduce

- On Blender create a Cube and a Sphere. Link the Sphere to the Cube and export both objects as a single `.glb` file.
- On Godot 4 setup a 3D scene to load the `.glb` file using the `GLTFDocument.generate_scene` function.
- Setup a camera to run the project.

The expected result is to see a Cube and a Sphere, but only the Cube is visible.

### Minimal reproduction project

Scene ready to test, and `.blend` file

[GLTFBug_v2.zip](https://github.com/godotengine/godot/files/10320776/GLTFBug_v2.zip)

MeshInstance3D *mesh_instance_node_3d = memnew(MeshInstance3D);
			Ref<ImporterMesh> mesh = mesh_3d->get_mesh();
			if (mesh.is_valid()) {
				Ref<ArrayMesh> array_mesh = mesh->get_mesh();
				mesh_instance_node_3d->set_name(node->get_name());
				mesh_instance_node_3d->set_transform(mesh_3d->get_transform());
				mesh_instance_node_3d->set_mesh(array_mesh);
				mesh_instance_node_3d->set_skin(mesh_3d->get_skin());
				mesh_instance_node_3d->set_skeleton_path(mesh_3d->get_skeleton_path());
				node->replace_by(mesh_instance_node_3d);
				delete_queue.push_back(node);
			} else {
				memdelete(mesh_instance_node_3d);
			}
		}
		int child_count = node->get_child_count();
		for (int i = 0; i < child_count; i++) {
			queue.push_back(node->get_child(i));
		}
		queue.pop_front();
	}
	while (!queue.is_empty()) {
		List<Node *>::Element *E = delete_queue.front();
		Node *node = E->get();
		memdelete(node);
		delete_queue.pop_front();
	}
	return OK;
}