### 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)

if (base_scene_idx >= 0) {
		Ref<PackedScene> ps = variants[base_scene_idx];
		if (ps.is_valid()) {
			return ps->get_state();
		}
	}
	return Ref<SceneState>();
}
void SceneState::update_instance_resource(String p_path, Ref<PackedScene> p_packed_scene) {
	ERR_FAIL_COND(p_packed_scene.is_null());
	for (const NodeData &nd : nodes) {
		if (nd.instance >= 0) {
			if (!(nd.instance & FLAG_INSTANCE_IS_PLACEHOLDER)) {
				int instance_id = nd.instance & FLAG_MASK;
				Ref<PackedScene> original_packed_scene = variants[instance_id];
				if (original_packed_scene.is_valid()) {
					if (original_packed_scene->get_path() == p_path) {
						variants.remove_at(instance_id);
						variants.insert(instance_id, p_packed_scene);
					}
				}
			}
		}
	}
}
int SceneState::find_node_by_path(const NodePath &p_node) const {