### Godot version

4.0-rc6

### System information

Fedora 37, Mesa Intel ADL GT2

### Issue description

Code that works as expected at runtime fails with Nil references to (assigned) exported vars in the editor:

![tool_global_position_error](https://user-images.githubusercontent.com/364501/222031460-ffb1ecbd-5175-4a42-8470-25285ba5f821.png)


### Steps to reproduce

Try to access the `global_position` of a `Node3D` that's assigned to an exported var.

See that it works at runtime.

See that it errors in the editor with:

> Invalid get index 'global_position' (on base: 'Nil').

### Minimal reproduction project

[tool_test.zip](https://github.com/godotengine/godot/files/10856640/tool_test.zip)

#include "packed_scene.h"
#include "core/config/engine.h"
#include "core/config/project_settings.h"
#include "core/core_string_names.h"
#include "core/io/missing_resource.h"
#include "core/io/resource_loader.h"
#include "core/templates/local_vector.h"
#include "scene/2d/node_2d.h"
#include "scene/3d/node_3d.h"
#include "scene/gui/control.h"
#include "scene/main/instance_placeholder.h"
#include "scene/main/missing_node.h"
#include "scene/property_utils.h"
#define PACKED_SCENE_VERSION 3
const String PackedScene::META_POINTER_PROPERTY_BASE = "metadata/_editor_prop_ptr_";
bool SceneState::can_instantiate() const {