### Godot version

v4.0.alpha11.official [afdae67cc] (when the feature was added) and newer (still happens in RC6)

### System information

Windows 10

### Issue description

I'm unable to handle when the user sets an exported node property (this feature: https://github.com/godotengine/godot/pull/62185) from a setter in the editor (tool script).

I don't know if this is intentional or not, but for me it was unexpected. I had to revert back to `NodePath`s.

### Steps to reproduce

- Create a scene
- Attach a script to a node
- Add `@tool` at the top of the script
- Export a node property with a setter, preferably with an easy way to see if it executed:
	```
	@export var node:Node:
		set (mod_value):
			prints("node", mod_value)
			node = mod_value
	```
- Save, close and open again the scene to make sure the tool script is running in the editor
- Set the node property from the inspector
- Observe that the setter didn't run

The setter is not bypassed when running the game, it is only bypassed in the editor.

We can compare with a `NodePath` property, which setter is not bypassed regardless if it is in the editor or in game runtime.

### Minimal reproduction project

[nodepath.zip](https://github.com/godotengine/godot/files/10840411/nodepath.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 {