### 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)

return use_edge_connections;
}
void NavigationRegion3D::set_navigation_layers(uint32_t p_navigation_layers) {
	if (navigation_layers == p_navigation_layers) {
		return;
	}
	navigation_layers = p_navigation_layers;
	NavigationServer3D::get_singleton()->region_set_navigation_layers(region, navigation_layers);
}
uint32_t NavigationRegion3D::get_navigation_layers() const {
	return navigation_layers;
}
void NavigationRegion3D::set_navigation_layer_value(int p_layer_number, bool p_value) {
	ERR_FAIL_COND_MSG(p_layer_number < 1, "Navigation layer number must be between 1 and 32 inclusive.");
	ERR_FAIL_COND_MSG(p_layer_number > 32, "Navigation layer number must be between 1 and 32 inclusive.");
	uint32_t _navigation_layers = get_navigation_layers();
	if (p_value) {
		_navigation_layers |= 1 << (p_layer_number - 1);
	} else {
		_navigation_layers &= ~(1 << (p_layer_number - 1));
	}
	set_navigation_layers(_navigation_layers);
}
bool NavigationRegion3D::get_navigation_layer_value(int p_layer_number) const {