### 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)

}
	}
#endif 
	emit_signal(SNAME("navigation_mesh_changed"));
	update_gizmos();
	update_configuration_warnings();
}
Ref<NavigationMesh> NavigationRegion3D::get_navigation_mesh() const {
	return navigation_mesh;
}
void NavigationRegion3D::set_navigation_map(RID p_navigation_map) {
	if (map_override == p_navigation_map) {
		return;
	}
	map_override = p_navigation_map;
	NavigationServer3D::get_singleton()->region_set_map(region, map_override);
}
RID NavigationRegion3D::get_navigation_map() const {
	if (map_override.is_valid()) {
		return map_override;
	} else if (is_inside_tree()) {
		return get_world_3d()->get_navigation_map();
	}
	return RID();
}
struct BakeThreadsArgs {
	NavigationRegion3D *nav_region = nullptr;
	Ref<NavigationMeshSourceGeometryData3D> source_geometry_data;
};
void _bake_navigation_mesh(void *p_user_data) {