### 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)

root = memnew(Window);
	root->set_min_size(Size2i(64, 64)); 
	root->set_process_mode(Node::PROCESS_MODE_PAUSABLE);
	root->set_name("root");
	root->set_title(GLOBAL_GET("application/config/name"));
#ifndef _3D_DISABLED
	if (!root->get_world_3d().is_valid()) {
		root->set_world_3d(Ref<World3D>(memnew(World3D)));
	}
	root->set_as_audio_listener_3d(true);
#endif 
	
	set_multiplayer(MultiplayerAPI::create_default_interface());
	root->set_as_audio_listener_2d(true);
	current_scene = nullptr;
	const int msaa_mode_2d = GLOBAL_DEF_BASIC(PropertyInfo(Variant::INT, "rendering/anti_aliasing/quality/msaa_2d", PROPERTY_HINT_ENUM, String::utf8("Disabled (Fastest),2× (Average),4× (Slow),8× (Slowest)")), 0);
	root->set_msaa_2d(Viewport::MSAA(msaa_mode_2d));
	const int msaa_mode_3d = GLOBAL_DEF_BASIC(PropertyInfo(Variant::INT, "rendering/anti_aliasing/quality/msaa_3d", PROPERTY_HINT_ENUM, String::utf8("Disabled (Fastest),2× (Average),4× (Slow),8× (Slowest)")), 0);
	root->set_msaa_3d(Viewport::MSAA(msaa_mode_3d));
	const bool transparent_background = GLOBAL_DEF("rendering/viewport/transparent_background", false);
	root->set_transparent_background(transparent_background);
	const int ssaa_mode = GLOBAL_DEF_BASIC(PropertyInfo(Variant::INT, "rendering/anti_aliasing/quality/screen_space_aa", PROPERTY_HINT_ENUM, "Disabled (Fastest),FXAA (Fast)"), 0);
	root->set_screen_space_aa(Viewport::ScreenSpaceAA(ssaa_mode));
	const bool use_taa = GLOBAL_DEF_BASIC("rendering/anti_aliasing/quality/use_taa", false);
	root->set_use_taa(use_taa);
	const bool use_debanding = GLOBAL_DEF("rendering/anti_aliasing/quality/use_debanding", false);
	root->set_use_debanding(use_debanding);
	const bool use_occlusion_culling = GLOBAL_DEF("rendering/occlusion_culling/use_occlusion_culling", false);
	root->set_use_occlusion_culling(use_occlusion_culling);
	float mesh_lod_threshold = GLOBAL_DEF(PropertyInfo(Variant::FLOAT, "rendering/mesh_lod/lod_change/threshold_pixels", PROPERTY_HINT_RANGE, "0,1024,0.1"), 1.0);