### Godot version

v4.0.beta12.mono.official [3c9bf4bc2]

### System information

Windows 10

### Issue description

When using GetTree().ChangeScene (or GetTree().ReloadCurrentScene), the orphan node count in Monitors goes up by the number of nodes in the target scene.

This effect is amplified when running a scene that has lots of nodes.


I've also tested this in the previous beta (v4.0.beta11.mono.official [91713ced8]) and confirmed the issue didn't exist there.

### Steps to reproduce

1. Run the included Minimal Reproduction Project.
2. Open the Debugger/Monitors tab.
3. Press "Space" to load Scene2.tcsn (2 Nodes).
 - Orphan nodes increases by 2.
5. Press "Space" to load Scene1.tcsn (3 Nodes).
 - Orphan nodes increases by 3.

### Minimal reproduction project

[MRP.zip](https://github.com/godotengine/godot/files/10415860/MRP.zip)

Vector<int> indices;
	for (int i = 0; i < 8 * 3; i++) {
		indices.push_back(diamond_faces[i]);
	}
	Vector<Vector3> vertices;
	for (int i = 0; i < 6; i++) {
		vertices.push_back(diamond[i] * 0.1);
	}
	Array arr;
	arr.resize(Mesh::ARRAY_MAX);
	arr[Mesh::ARRAY_VERTEX] = vertices;
	arr[Mesh::ARRAY_INDEX] = indices;
	debug_contact_mesh->add_surface_from_arrays(Mesh::PRIMITIVE_TRIANGLES, arr);
	debug_contact_mesh->surface_set_material(0, mat);
	return debug_contact_mesh;
}
void SceneTree::set_pause(bool p_enabled) {
	if (p_enabled == paused) {
		return;
	}
	paused = p_enabled;
	NavigationServer3D::get_singleton()->set_active(!p_enabled);
	PhysicsServer3D::get_singleton()->set_active(!p_enabled);
	PhysicsServer2D::get_singleton()->set_active(!p_enabled);
	if (get_root()) {
		get_root()->_propagate_pause_notification(p_enabled);
	}
}
bool SceneTree::is_paused() const {