### Godot version

v4.0.3.stable.official [5222a99f5]

### System information

Mac

### Issue description

The following code will not print any vertices, nor polygons. 
The `NavigationMesh` resource will not be saved correctly.

Even though we specify `bake_navigation_mesh(false)` (on the main thread)

```gdscript
func _ready() -> void:
	var navreg = $NavigationRegion3D
	navreg.bake_navigation_mesh(false)
	
	print(navreg.navmesh.get_vertices())
	print(navreg.navmesh.get_polygon_count())

	var to_save = preload("res://testresource.gd").new(navreg.navmesh)
	ResourceSaver.save(
		to_save,
		"output.tres",
		ResourceSaver.SaverFlags.FLAG_BUNDLE_RESOURCES
	)
```

### Steps to reproduce

1. Download minimal repo below
2. Run the repo
3. Check the console
4. Check `output.tres`

<img width="316" alt="Screenshot 2023-06-03 at 19 05 22" src="https://github.com/godotengine/godot/assets/100964/83ea661d-1c5a-4044-b9cc-2a5434a89280">

<img width="1028" alt="Screenshot 2023-06-03 at 19 05 34" src="https://github.com/godotengine/godot/assets/100964/cb099d0c-f626-48a4-b4f4-9a57b7988df1">


### Minimal reproduction project

[test-navmesh.zip](https://github.com/godotengine/godot/files/11642578/test-navmesh.zip)

if (bake_thread.is_started()) {
		bake_thread.wait_to_finish();
	}
	if (navigation_mesh.is_valid()) {
		navigation_mesh->disconnect_changed(callable_mp(this, &NavigationRegion3D::_navigation_mesh_changed));
	}
	ERR_FAIL_NULL(NavigationServer3D::get_singleton());
	NavigationServer3D::get_singleton()->free(region);
#ifdef DEBUG_ENABLED
	NavigationServer3D::get_singleton()->disconnect(SNAME("map_changed"), callable_mp(this, &NavigationRegion3D::_navigation_map_changed));
	NavigationServer3D::get_singleton()->disconnect(SNAME("navigation_debug_changed"), callable_mp(this, &NavigationRegion3D::_update_debug_mesh));
	NavigationServer3D::get_singleton()->disconnect(SNAME("navigation_debug_changed"), callable_mp(this, &NavigationRegion3D::_update_debug_edge_connections_mesh));
	ERR_FAIL_NULL(RenderingServer::get_singleton());
	if (debug_instance.is_valid()) {
		RenderingServer::get_singleton()->free(debug_instance);
	}
	if (debug_mesh.is_valid()) {
		RenderingServer::get_singleton()->free(debug_mesh->get_rid());
	}
	if (debug_edge_connections_instance.is_valid()) {
		RenderingServer::get_singleton()->free(debug_edge_connections_instance);
	}
	if (debug_edge_connections_mesh.is_valid()) {
		RenderingServer::get_singleton()->free(debug_edge_connections_mesh->get_rid());
	}
#endif 
}
#ifdef DEBUG_ENABLED
void NavigationRegion3D::_update_debug_mesh() {