### 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->set_positional_shadow_atlas_16_bits(shadowmap_16_bits);
	root->set_positional_shadow_atlas_quadrant_subdiv(0, Viewport::PositionalShadowAtlasQuadrantSubdiv(atlas_q0));
	root->set_positional_shadow_atlas_quadrant_subdiv(1, Viewport::PositionalShadowAtlasQuadrantSubdiv(atlas_q1));
	root->set_positional_shadow_atlas_quadrant_subdiv(2, Viewport::PositionalShadowAtlasQuadrantSubdiv(atlas_q2));
	root->set_positional_shadow_atlas_quadrant_subdiv(3, Viewport::PositionalShadowAtlasQuadrantSubdiv(atlas_q3));
	Viewport::SDFOversize sdf_oversize = Viewport::SDFOversize(int(GLOBAL_DEF(PropertyInfo(Variant::INT, "rendering/2d/sdf/oversize", PROPERTY_HINT_ENUM, "100%,120%,150%,200%"), 1)));
	root->set_sdf_oversize(sdf_oversize);
	Viewport::SDFScale sdf_scale = Viewport::SDFScale(int(GLOBAL_DEF(PropertyInfo(Variant::INT, "rendering/2d/sdf/scale", PROPERTY_HINT_ENUM, "100%,50%,25%"), 1)));
	root->set_sdf_scale(sdf_scale);
#ifndef _3D_DISABLED
	{ // Load default fallback environment.
		// Get possible extensions.
		List<String> exts;
		ResourceLoader::get_recognized_extensions_for_type("Environment", &exts);
		String ext_hint;
		for (const String &E : exts) {
			if (!ext_hint.is_empty()) {
				ext_hint += ",";
			}
			ext_hint += "*." + E;
		}
		// Get path.
		String env_path = GLOBAL_DEF(PropertyInfo(Variant::STRING, "rendering/environment/defaults/default_environment", PROPERTY_HINT_FILE, ext_hint), "");
		// Setup property.
		env_path = env_path.strip_edges();
		if (!env_path.is_empty()) {
			Ref<Environment> env = ResourceLoader::load(env_path);
			if (env.is_valid()) {
				root->get_world_3d()->set_fallback_environment(env);
			} else {