### 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)

#include "gltf_document_extension_convert_importer_mesh.h"
#include "scene/3d/importer_mesh_instance_3d.h"
#include "scene/3d/mesh_instance_3d.h"
#include "scene/resources/importer_mesh.h"
void GLTFDocumentExtensionConvertImporterMesh::_bind_methods() {
}
Error GLTFDocumentExtensionConvertImporterMesh::import_post(Ref<GLTFState> p_state, Node *p_root) {
	ERR_FAIL_NULL_V(p_root, ERR_INVALID_PARAMETER);
	ERR_FAIL_NULL_V(p_state, ERR_INVALID_PARAMETER);
	List<Node *> queue;
	queue.push_back(p_root);
	List<Node *> delete_queue;
	while (!queue.is_empty()) {
		List<Node *>::Element *E = queue.front();
		Node *node = E->get();
		ImporterMeshInstance3D *mesh_3d = cast_to<ImporterMeshInstance3D>(node);
		if (mesh_3d) {