### 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)

return debug_paths_width;
}
Ref<Material> SceneTree::get_debug_paths_material() {
	if (debug_paths_material.is_valid()) {
		return debug_paths_material;
	}
	Ref<StandardMaterial3D> _debug_material = Ref<StandardMaterial3D>(memnew(StandardMaterial3D));
	_debug_material->set_shading_mode(StandardMaterial3D::SHADING_MODE_UNSHADED);
	_debug_material->set_transparency(StandardMaterial3D::TRANSPARENCY_ALPHA);
	_debug_material->set_flag(StandardMaterial3D::FLAG_SRGB_VERTEX_COLOR, true);
	_debug_material->set_flag(StandardMaterial3D::FLAG_ALBEDO_FROM_VERTEX_COLOR, true);
	_debug_material->set_albedo(get_debug_paths_color());
	debug_paths_material = _debug_material;
	return debug_paths_material;
}
Ref<Material> SceneTree::get_debug_collision_material() {
	if (collision_material.is_valid()) {
		return collision_material;
	}
	Ref<StandardMaterial3D> line_material = Ref<StandardMaterial3D>(memnew(StandardMaterial3D));
	line_material->set_shading_mode(StandardMaterial3D::SHADING_MODE_UNSHADED);
	line_material->set_transparency(StandardMaterial3D::TRANSPARENCY_ALPHA);
	line_material->set_flag(StandardMaterial3D::FLAG_SRGB_VERTEX_COLOR, true);
	line_material->set_flag(StandardMaterial3D::FLAG_ALBEDO_FROM_VERTEX_COLOR, true);
	line_material->set_albedo(get_debug_collisions_color());
	collision_material = line_material;
	return collision_material;
}
Ref<ArrayMesh> SceneTree::get_debug_contact_mesh() {