### 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 (!NavigationServer3D::get_singleton()->get_debug_navigation_enabled()) {
		if (debug_edge_connections_instance.is_valid()) {
			RS::get_singleton()->instance_set_visible(debug_edge_connections_instance, false);
		}
		return;
	}
	if (!is_inside_tree()) {
		return;
	}
	if (!use_edge_connections || !NavigationServer3D::get_singleton()->map_get_use_edge_connections(get_world_3d()->get_navigation_map())) {
		if (debug_edge_connections_instance.is_valid()) {
			RS::get_singleton()->instance_set_visible(debug_edge_connections_instance, false);
		}
		return;
	}
	if (!navigation_mesh.is_valid()) {
		if (debug_edge_connections_instance.is_valid()) {
			RS::get_singleton()->instance_set_visible(debug_edge_connections_instance, false);