### 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)

if (debug_contact_mesh.is_valid()) {
		return debug_contact_mesh;
	}
	debug_contact_mesh = Ref<ArrayMesh>(memnew(ArrayMesh));
	Ref<StandardMaterial3D> mat = Ref<StandardMaterial3D>(memnew(StandardMaterial3D));
	mat->set_shading_mode(StandardMaterial3D::SHADING_MODE_UNSHADED);
	mat->set_transparency(StandardMaterial3D::TRANSPARENCY_ALPHA);
	mat->set_flag(StandardMaterial3D::FLAG_SRGB_VERTEX_COLOR, true);
	mat->set_flag(StandardMaterial3D::FLAG_ALBEDO_FROM_VERTEX_COLOR, true);
	mat->set_albedo(get_debug_collision_contact_color());
	Vector3 diamond[6] = {
		Vector3(-1, 0, 0),
		Vector3(1, 0, 0),
		Vector3(0, -1, 0),
		Vector3(0, 1, 0),
		Vector3(0, 0, -1),
		Vector3(0, 0, 1)
	};
	
	int diamond_faces[8 * 3] = {
		0, 2, 4,
		0, 3, 4,
		1, 2, 4,
		1, 3, 4,
		0, 2, 5,
		0, 3, 5,
		1, 2, 5,
		1, 3, 5,
	};